Mercurial > repos > estrain > metaphlan_gt

annotate metaphlan_gt.xml @ 0:a7bd05df0bea draft default tip

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planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
author estrain
date Fri, 13 Mar 2026 12:06:00 +0000
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a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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1 <tool id="metaphlan_gt" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
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2 <description>to profile the composition of microbial communities</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 <xml name="tax_lev">
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7 <conditional name="tax_lev">
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8 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
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9 <option value="a" selected="true">All taxonomic levels</option>
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10 <option value="k">Kingdoms only</option>
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11 <option value="p">Phyla only</option>
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12 <option value="c">Classes only</option>
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13 <option value="o">Orders only</option>
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14 <option value="f">Families only</option>
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15 <option value="g">Genera only</option>
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16 <option value="s">Species only</option>
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17 </param>
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18 <when value="a">
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19 <param name="split_levels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
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20 </when>
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21 <when value="k"/>
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22 <when value="p"/>
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23 <when value="c"/>
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24 <when value="o"/>
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25 <when value="f"/>
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26 <when value="g"/>
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27 <when value="s"/>
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28 </conditional>
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29 </xml>
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30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz</token>
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31 </macros>
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32 <expand macro="requirements"/>
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33 <version_command>metaphlan -v</version_command>
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34 <command detect_errors="aggressive"><![CDATA[
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35 #if $inputs.in.selector == "raw"
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36 #if $inputs.in.raw_in.selector == "single"
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37 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext
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38 #if $full_ext.endswith("gz")
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39 #set $file_path="in"
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40 zcat '$inputs.in.raw_in.in' > '$file_path' &&
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41 #else if $full_ext.endswith("bz2")
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42 #set $file_path="in"
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43 bzcat '$inputs.in.raw_in.in' > '$file_path' &&
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44 #else
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45 #set $file_path="'%s'" % $inputs.in.raw_in.in
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46 #end if
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47 #else if $inputs.in.raw_in.selector == "multiple"
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48 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext
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49 #set file_path=""
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50 #set sep=""
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51 #for $i, $f in enumerate($inputs.in.raw_in.in)
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52 #if $f.datatype.file_ext != $full_ext
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53 echo "Different datatypes for input files" &&
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54 exit 1
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55 #end if
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56 #if $full_ext.endswith("gz")
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57 #set fp="input_%s" % ($i)
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58 zcat '$f' > '$fp' &&
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59 #else if $full_ext.endswith("bz2")
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60 #set fp="input_%s" % ($i)
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61 bzcat '$f' > '$fp' &&
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62 #else
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63 #set fp=$f
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64 #end if
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65 #set $file_path+="'%s%s'" % ($sep, $fp)
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66 #set $sep=","
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67 #end for
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68 #else if $inputs.in.raw_in.selector == "paired"
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69 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext
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70 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext
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71 echo "Different datatypes for input paired-end files" &&
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72 exit 1
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73 #end if
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74 #if $full_ext.endswith("gz")
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75 zcat '$inputs.in.raw_in.in_f' > 'in_f' &&
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76 zcat '$inputs.in.raw_in.in_r' > 'in_r' &&
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77 #else if $full_ext.endswith("bz2")
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78 bzcat '$inputs.in.raw_in.in_f' > 'in_f' &&
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79 bzcat '$inputs.in.raw_in.in_r' > 'in_r' &&
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80 #else:
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81 ln -s '$inputs.in.raw_in.in_f' 'in_f' &&
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82 ln -s '$inputs.in.raw_in.in_r' 'in_r' &&
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83 #end if
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84 ## paired data has by default no special treatment, i.e. it is given as comma separated list
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85 ## except iff paired subsampling where -1 and -2 must be used
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86 #if $subsample.selector == 'paired'
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87 #set file_path="-1 in_f -2 in_r"
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88 #else
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89 #set file_path="in_f,in_r"
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90 #end if
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91 #else if $inputs.in.raw_in.selector == "paired_collection"
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92 #set full_ext=$inputs.in.raw_in.in.forward.ext
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93 #if $full_ext != $inputs.in.raw_in.in.reverse.ext
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94 echo "Different datatypes for input paired-end files" &&
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95 exit 1
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96 #end if
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97 #if $full_ext.endswith("gz")
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98 zcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
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99 zcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
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100 #else if $full_ext.endswith("bz2")
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101 bzcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
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102 bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
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103 #else
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104 ln -s '$inputs.in.raw_in.in.forward' 'in_f' &&
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105 ln -s '$inputs.in.raw_in.in.reverse' 'in_r' &&
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106 #end if
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107 #if $subsample.selector == 'paired'
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108 #set file_path="-1 in_f -2 in_r"
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109 #else
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110 #set file_path="in_f,in_r"
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111 #end if
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112 #end if
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113
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114 #if $full_ext.startswith("fastq")
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115 #set ext='fastq'
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116 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))
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117 #set ext='fasta'
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118 #else
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119 #set ext=$full_ext
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120 #end if
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121 #end if
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122
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123 #if $inputs.db.db_selector == "history"
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124 mkdir 'ref_db' &&
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125 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db' &&
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126 python
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127 '$__tool_directory__/customizemetadata.py'
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128 transform_json_to_pkl
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129 --json '$inputs.db.mpa_pkl'
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130 --pkl 'ref_db/custom_db.pkl' &&
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131 #end if
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132
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133 metaphlan
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134 #if $inputs.in.selector == "raw"
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135 $file_path
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136 --input_type '$ext'
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137 --read_min_len $inputs.in.read_min_len
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138 --bt2_ps '$inputs.in.mapping.bt2_ps'
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139 --min_mapq_val $inputs.in.mapping.min_mapq_val
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140 #if $ext == "sam"
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141 --nreads \$(cat '$file_path' | grep -c -v '^@')
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142 #end if
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143 #else
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144 '$inputs.in.in'
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145 --input_type '$inputs.in.selector'
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146 #if $inputs.in.selector == "sam"
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147 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')
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148 #end if
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149 #end if
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150 #if $inputs.db.db_selector == "cached"
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151 --bowtie2db '$inputs.db.cached_db.fields.path'
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152 --index '$inputs.db.cached_db.fields.dbkey'
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153 #else
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154 --bowtie2db 'ref_db/'
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155 --index 'custom_db'
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156 #end if
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157 -t '$analysis.analysis_type.t'
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158 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
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159 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
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160 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
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161 --clade '$analysis.analysis_type.clade'
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162 #if str($analysis.analysis_type.min_ab) != ''
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163 --min_ab $analysis.analysis_type.min_ab
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164 #end if
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165 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
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166 --nreads $$analysis.analysis_type.nreads
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167 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
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168 --pres_th $analysis.analysis_type.pres_th
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169 #end if
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170 --min_cu_len $analysis.min_cu_len
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171 #if str($analysis.min_alignment_len) != ''
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172 --min_alignment_len $analysis.min_alignment_len
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173 #end if
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174 #if 'add_viruses' in $analysis.organism_profiling
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175 --add_viruses
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176 #end if
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177 #if 'ignore_eukaryotes' in $analysis.organism_profiling
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178 --ignore_eukaryotes
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179 #end if
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180 #if 'ignore_bacteria' in $analysis.organism_profiling
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181 --ignore_bacteria
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182 #end if
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183 #if 'ignore_archaea' in $analysis.organism_profiling
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184 --ignore_archaea
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185 #end if
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186 --stat $analysis.stat
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187 --stat_q $analysis.stat_q
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188 --perc_nonzero $analysis.perc_nonzero
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189 #if $analysis.ignore_markers
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190 --ignore_markers '$analysis.ignore_markers'
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191 #end if
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192 $analysis.avoid_disqm
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193 --sample_id_key '$out.sample_id_key'
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194 --sample_id '$out.sample_id'
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195 $out.use_group_representative
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196 $out.legacy_output
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197 $out.CAMI_format_output
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198 $out.unclassified_estimation
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199 -o '$output_file'
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200 --bowtie2out 'bowtie2out'
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201 -s 'sam_output_file'
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202 --biom '$biom_output_file'
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203 --nproc \${GALAXY_SLOTS:-4}
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204 #if $viral_analysis.profile_vsc
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205 $viral_analysis.profile_vsc
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206 --vsc_out '$vcs_breath_coverage'
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207 --vsc_breadth $viral_analysis.vsc_breadth
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208 #end if
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209
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210 #if $subsample.selector != "no"
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211 #if $subsample.selector == "single"
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212 --subsampling $subsample.subsampling
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213 #else
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214 --subsampling_paired $subsample.subsampling_paired
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215 #end if
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216 $subsample.mapping_subsampling
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217 #if $subsample.subsampling_seed
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218 --subsampling_seed $subsample.subsampling_seed
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219 #end if
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220 --subsampling_output subsampled.out
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221 #end if
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222
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223 #if $test == "false"
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224 --offline
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225 #end if
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226
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227
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228 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
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229 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
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230 &&
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231 mkdir 'split_levels'
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232 &&
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233 python '$__tool_directory__/formatoutput.py'
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234 split_levels
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235 --metaphlan_output '$output_file'
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236 --outdir 'split_levels'
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237 $out.legacy_output
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238 #end if
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239 #end if
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240
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241 #if $out.krona_output
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242 &&
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243 python '$__tool_directory__/formatoutput.py'
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244 format_for_krona
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245 --metaphlan_output '$output_file'
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246 --krona_output '$krona_output_file'
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247 #end if
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248 ]]></command>
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249 <inputs>
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250 <section name="inputs" title="Inputs" expanded="true">
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251 <conditional name="in">
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252 <param name="selector" type="select" label="Input(s)">
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253 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
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254 <option value="sam">Externally BowTie2-mapped SAM file</option>
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255 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
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256 </param>
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257 <when value="raw">
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258 <conditional name="raw_in">
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259 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
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260 <option value="single" selected="true">One single-end file</option>
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261 <option value="multiple">Multiple single-end files</option>
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262 <option value="paired_collection">Paired-end collection</option>
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263 <option value="paired">Paired-end files</option>
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264 </param>
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265 <when value="single">
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266 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
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267 </when>
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268 <when value="multiple">
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269 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ files with microbiota reads" multiple="true"/>
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270 </when>
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271 <when value="paired_collection">
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272 <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads" collection_type="paired"/>
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273 </when>
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274 <when value="paired">
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275 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
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276 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>
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277 </when>
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278 </conditional>
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279 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>
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280 <section name="mapping" title="Mapping" expanded="true">
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281 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">
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282 <option value="sensitive">Sensitive</option>
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283 <option value="very-sensitive" selected="true">Very sensitive</option>
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284 <option value="sensitive-local">Sensitive local</option>
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285 <option value="very-sensitive-local">Very sensitive local</option>
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286 </param>
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287 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>
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288 </section>
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289 </when>
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290 <when value="sam">
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291 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
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292 </when>
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293 <when value="bowtie2out">
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294 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions &gt;3.0"/>
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295 </when>
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296 </conditional>
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297 <conditional name="db">
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298 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
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299 <option value="cached" selected="true">Locally cached</option>
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300 <option value="history">From history</option>
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301 </param>
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302 <when value="cached">
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303 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
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304 <options from_data_table="@IDX_DATA_TABLE@">
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305 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
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306 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
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307 </options>
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308 </param>
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309 </when>
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310 <when value="history">
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311 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
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312 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
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313 </when>
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314 </conditional>
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315 </section>
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316 <section name="analysis" title="Analysis" expanded="true">
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317 <conditional name="analysis_type">
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318 <param argument="-t" type="select" label="Type of analysis to perform">
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319 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
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320 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>
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321 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
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322 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
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323 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
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324 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when &gt; 0.0 and normalized by microbiota size if number of reads is specified)</option>
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325 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
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326 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
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327 </param>
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328 <when value="rel_ab">
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329 <expand macro="tax_lev"/>
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330 </when>
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331 <when value="rel_ab_w_read_stats">
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332 <expand macro="tax_lev"/>
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333 </when>
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334 <when value="reads_map"/>
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335 <when value="clade_profiles"/>
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336 <when value="clade_specific_strain_tracker">
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337 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present" help="Markers are also extracted for subclades"/>
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338 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
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339 </when>
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340 <when value="marker_ab_table">
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341 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
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342 </when>
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343 <when value="marker_counts"/>
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344 <when value="marker_pres_table">
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345 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
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346 </when>
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347 </conditional>
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348 <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
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349 <param argument="--min_alignment_len" type="integer" optional="true" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
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350 <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true">
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351 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
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352 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
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353 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
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354 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
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355 </param>
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356 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
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357 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
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358 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
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359 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
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360 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>
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361 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>
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362 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>
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363 <option value="med">med: Median of length-normalized marker counts</option>
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364 </param>
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365 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
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366 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
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367 <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>
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368 <param argument="--avoid_disqm" type="boolean" truevalue="--avoid_disqm" falsevalue="" checked="true" label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?" help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
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369 </section>
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370 <conditional name="subsample">
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371 <param name="selector" type="select" label="Subsample" help="Subsampling only works for fastq input">
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372 <option value="no">No</option>
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373 <option value="single">Yes: specify number of reads</option>
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374 <option value="paired">Yes: specify number of paired reads</option>
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375 </param>
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376 <when value="no"/>
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377 <when value="single">
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378 <param argument="--subsampling" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of reads to be considered"/>
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379 <expand macro="subsample_common"/>
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380 </when>
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381 <when value="paired">
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382 <param argument="--subsampling_paired" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/>
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383 <expand macro="subsample_common"/>
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384 </when>
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385 </conditional>
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386 <conditional name="viral_analysis">
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387 <param argument="--profile_vsc" type="select" label="Profile Viruses with VSCs approach">
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388 <option value="--profile_vsc">Yes (requires FASTQ input and reference data with VSG fasta)</option>
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389 <option value="" selected="true">No</option>
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390 </param>
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391 <when value="--profile_vsc">
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392 <param argument="--vsc_breadth" type="float" min="0" max="1" value="0.75" label="Minimum Breadth of Coverage" help="Minimum coverage (fraction) for a Viral Group to be reported."/>
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393 </when>
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394 <when value=""/>
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395 </conditional>
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396 <section name="out" title="Outputs" expanded="true">
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397 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
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398 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
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399 <param argument="--use_group_representative" type="boolean" truevalue="--use_group_representative" falsevalue="" checked="false" label="Use a species as representative for species groups?"/>
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400 <param argument="--legacy-output" type="boolean" truevalue="--legacy-output" falsevalue="" checked="false" label="Old MetaPhlAn2 two columns output?"/>
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401 <param argument="--CAMI_format_output" type="boolean" truevalue="--CAMI_format_output" falsevalue="" checked="false" label="Report the profiling using the CAMI output format?"/>
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402 <param argument="--unclassified_estimation" type="boolean" truevalue="--unclassified_estimation" falsevalue="" checked="false" label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
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403 <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/>
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404 </section>
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405 <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) -->
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406 <param name="test" type="hidden" value="false"/>
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407 </inputs>
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408 <outputs>
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409 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/>
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410 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/>
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411 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels">
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412 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
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413 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
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414 </collection>
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415 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
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416 <filter>out['krona_output']</filter>
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417 </data>
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418 <data name="vcs_breath_coverage" format="tabular" label="${tool.name} on ${on_string}: VSCs breadth-of-coverage">
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419 <filter>viral_analysis['profile_vsc']</filter>
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420 </data>
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421 <data name="subsample_single" format="fastqsanger" from_work_dir="subsampled.out" label="${tool.name} on ${on_string}: Subsampled reads">
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422 <filter>subsample['selector'] == 'single'</filter>
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423 </data>
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424 <collection name="subsample_paired" type="paired" label="${tool.name} on ${on_string}: Subsampled paired reads">
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425 <data name="forward" format="fastqsanger" from_work_dir="subsampled.R1.out"/>
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426 <data name="reverse" format="fastqsanger" from_work_dir="subsampled.R2.out"/>
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427 <filter>subsample['selector'] == 'paired'</filter>
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428 </collection>
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429 </outputs>
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430 <tests>
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431 <!-- Single GZ file, Cached db -->
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432 <test expect_num_outputs="6">
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433 <section name="inputs">
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434 <conditional name="in">
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435 <param name="selector" value="raw"/>
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436 <conditional name="raw_in">
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437 <param name="selector" value="single"/>
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438 <param name="in" value="no_taxon_input.fasta"/>
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439 </conditional>
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440 <param name="read_min_len" value="70"/>
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441 <section name="mapping">
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442 <param name="bt2_ps" value="sensitive"/>
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443 <param name="min_mapq_val" value="5"/>
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444 </section>
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445 </conditional>
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446 <conditional name="db">
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447 <param name="db_selector" value="cached"/>
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448 <param name="cached_db" value="test-db-20210409"/>
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449 </conditional>
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450 </section>
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451 <section name="analysis">
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452 <conditional name="analysis_type">
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453 <param name="t" value="rel_ab"/>
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454 <conditional name="tax_lev">
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455 <param name="tax_lev" value="a"/>
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456 <param name="split_levels" value="true"/>
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457 </conditional>
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458 </conditional>
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459 <param name="min_cu_len" value="2000"/>
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460 <param name="organism_profiling" value="add_viruses"/>
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461 <param name="stat" value="avg_g"/>
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462 <param name="stat_q" value="0.2"/>
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463 <param name="perc_nonzero" value="0.33"/>
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464 <param name="avoid_disqm" value="true"/>
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estrain
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diff changeset
465 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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466 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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467 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
468 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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469 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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470 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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471 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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472 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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473 <param name="krona_output" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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474 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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475 <output name="output_file" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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476 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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477 <has_text text="UNCLASSIFIED"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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478 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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479 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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480 <output name="biom_output_file" ftype="biom1">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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481 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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482 <not_has_text text="k__Bacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
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483 <not_has_text text="p__Actinobacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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484 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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485 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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486 <output_collection name="levels" type="list">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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487 <element name="all" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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488 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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489 <has_text text="class"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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490 <has_n_columns n="17"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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491 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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492 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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diff changeset
493 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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494 <element name="class" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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495 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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496 <has_text text="class_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
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497 <not_has_text text="phylum_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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498 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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499 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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500 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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501 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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502 <element name="family" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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503 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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504 <has_text text="family_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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505 <not_has_text text="order"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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506 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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507 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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508 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
509 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
510 <element name="genus" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
511 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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512 <has_text text="genus_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
513 <not_has_text text="family"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
514 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
515 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
516 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
517 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
518 <element name="kingdom" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
519 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
520 <has_text text="kingdom_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
521 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
522 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
523 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
524 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
525 <element name="order" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
526 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
527 <has_text text="order_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
528 <not_has_text text="class_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
529 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
530 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
531 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
532 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
533 <element name="phylum" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
534 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
535 <has_text text="phylum_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
536 <not_has_text text="kingdom_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
537 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
538 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
539 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
540 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
541 <element name="species" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
542 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
543 <has_text text="species_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
544 <not_has_text text="genus"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
545 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
546 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
547 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
548 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
549 <element name="strains" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
550 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
551 <has_text text="strains_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
552 <not_has_text text="species_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
553 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
554 <has_n_lines n="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
555 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
556 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
557 </output_collection>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
558 <output name="krona_output_file" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
559 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
560 <not_has_text text="k__Bacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
561 <has_n_lines n="1" delta="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
562 <has_size value="1" delta="1"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
563 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
564 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
565 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
566 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
567 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
568 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
569 <!-- Single GZ file, Cached db -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
570 <test expect_num_outputs="6">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
571 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
572 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
573 <param name="selector" value="raw"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
574 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
575 <param name="selector" value="single"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
576 <param name="in" value="SRS014464-Anterior_nares.fasta.gz"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
577 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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578 <param name="read_min_len" value="70"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
579 <section name="mapping">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
580 <param name="bt2_ps" value="sensitive"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
581 <param name="min_mapq_val" value="5"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
582 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
583 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
584 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
585 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
586 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
587 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
588 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
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589 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
590 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
591 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
592 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
593 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
594 <param name="split_levels" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
595 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
596 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
597 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
598 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
599 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
600 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
601 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
602 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
603 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
604 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
605 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
606 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
607 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
608 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
609 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
610 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
611 <param name="krona_output" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
612 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
613 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
614 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
615 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
616 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
617 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
618 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
619 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
620 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
621 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
622 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
623 <output_collection name="levels" type="list">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
624 <element name="all" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
625 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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626 <has_text text="Gammaproteobacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
627 <has_text text="Corynebacterium accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
628 <has_n_columns n="17"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
629 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
630 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
631 <element name="class" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
632 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
633 <has_text text="class_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
634 <not_has_text text="phylum_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
635 <has_text text="Actinobacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
636 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
637 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
638 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
639 <element name="family" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
640 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
641 <has_text text="family_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
642 <not_has_text text="order"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
643 <has_text text="Propionibacteriaceae"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
644 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
645 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
646 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
647 <element name="genus" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
648 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
649 <has_text text="genus_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
650 <not_has_text text="family"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
651 <has_text text="Cutibacterium"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
652 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
653 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
654 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
655 <element name="kingdom" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
656 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
657 <has_text text="kingdom_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
658 <has_text text="Bacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
659 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
660 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
661 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
662 <element name="order" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
663 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
664 <has_text text="order_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
665 <not_has_text text="class_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
666 <has_text text="Propionibacteriales"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
667 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
668 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
669 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
670 <element name="phylum" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
671 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
672 <has_text text="phylum_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
673 <not_has_text text="kingdom_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
674 <has_text text="Firmicutes"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
675 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
676 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
677 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
678 <element name="species" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
679 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
680 <has_text text="species_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
681 <not_has_text text="genus"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
682 <has_text text="Corynebacterium accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
683 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
684 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
685 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
686 <element name="strains" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
687 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
688 <has_text text="strains_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
689 <not_has_text text="species_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
690 <has_n_columns n="3"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
691 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
692 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
693 </output_collection>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
694 <output name="krona_output_file" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
695 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
696 <not_has_text text="k__Bacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
697 <has_text text="Corynebacterium accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
698 <has_n_columns n="9"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
699 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
700 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
701 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
702 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
703 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
704 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
705 <!-- Multiple GZ file, Local db-->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
706 <test expect_num_outputs="4">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
707 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
708 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
709 <param name="selector" value="raw"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
710 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
711 <param name="selector" value="multiple"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
712 <param name="in" value="SRS014464-Anterior_nares.fasta.gz,SRS014464-Anterior_nares.fasta.gz"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
713 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
714 <param name="read_min_len" value="70"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
715 <section name="mapping">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
716 <param name="bt2_ps" value="sensitive"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
717 <param name="min_mapq_val" value="5"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
718 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
719 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
720 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
721 <param name="db_selector" value="history"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
722 <param name="bowtie2db" value="test-db.fasta"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
723 <param name="mpa_pkl" value="test-db.json"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
724 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
725 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
726 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
727 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
728 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
729 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
730 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
731 <param name="split_levels" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
732 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
733 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
734 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
735 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
736 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
737 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
738 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
739 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
740 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
741 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
742 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
743 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
744 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
745 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
746 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
747 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
748 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
749 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
750 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
751 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
752 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
753 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
754 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
755 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
756 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
757 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
758 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
759 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
760 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
761 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
762 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
763 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
764 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
765 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
766 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
767 <!-- Paired GZ file, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
768 <test expect_num_outputs="7">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
769 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
770 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
771 <param name="selector" value="raw"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
772 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
773 <param name="selector" value="paired"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
774 <param name="in_f" value="SRS014464-Anterior_nares.fastq.gz"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
775 <param name="in_r" value="SRS014464-Anterior_nares.fastq.gz"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
776 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
777 <param name="read_min_len" value="70"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
778 <section name="mapping">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
779 <param name="bt2_ps" value="sensitive"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
780 <param name="min_mapq_val" value="5"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
781 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
782 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
783 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
784 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
785 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
786 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
787 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
788 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
789 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
790 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
791 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
792 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
793 <param name="split_levels" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
794 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
795 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
796 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
797 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
798 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
799 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
800 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
801 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
802 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
803 <conditional name="subsample">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
804 <param name="selector" value="paired"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
805 <param name="subsampling_paired" value="20257"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
806 <param name="subsampling_seed" value="42"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
807 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
808 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
809 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
810 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
811 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
812 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
813 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
814 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
815 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
816 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
817 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
818 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
819 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
820 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
821 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
822 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
823 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
824 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
825 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
826 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
827 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
828 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
829 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
830 <output_collection name="subsample_paired" type="paired">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
831 <element name="forward">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
832 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
833 <has_line_matching expression="^@.*" n="10128"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
834 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
835 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
836 <element name="reverse">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
837 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
838 <has_line_matching expression="^@.*" n="10128"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
839 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
840 </element>
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parents:
diff changeset
841 </output_collection>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
842 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
843 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
844 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
845 </test>
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parents:
diff changeset
846 <!-- Paired GZ file as collection, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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diff changeset
847 <test expect_num_outputs="7">
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parents:
diff changeset
848 <section name="inputs">
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parents:
diff changeset
849 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
850 <param name="selector" value="raw"/>
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parents:
diff changeset
851 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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852 <param name="selector" value="paired_collection"/>
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parents:
diff changeset
853 <param name="in">
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diff changeset
854 <collection type="paired" name="pair">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
855 <element name="forward" value="SRS014464-Anterior_nares.fastq.gz"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
856 <element name="reverse" value="SRS014464-Anterior_nares.fastq.gz"/>
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857 </collection>
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858 </param>
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parents:
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859 </conditional>
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parents:
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860 <param name="read_min_len" value="70"/>
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parents:
diff changeset
861 <section name="mapping">
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parents:
diff changeset
862 <param name="bt2_ps" value="sensitive"/>
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parents:
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863 <param name="min_mapq_val" value="5"/>
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parents:
diff changeset
864 </section>
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parents:
diff changeset
865 </conditional>
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parents:
diff changeset
866 <conditional name="db">
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parents:
diff changeset
867 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
868 <param name="cached_db" value="test-db-20210409"/>
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parents:
diff changeset
869 </conditional>
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parents:
diff changeset
870 </section>
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parents:
diff changeset
871 <section name="analysis">
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parents:
diff changeset
872 <conditional name="analysis_type">
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parents:
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873 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
874 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
875 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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876 <param name="split_levels" value="false"/>
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parents:
diff changeset
877 </conditional>
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parents:
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878 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
879 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
880 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
881 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
882 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
883 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
884 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
885 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
886 <conditional name="subsample">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
887 <param name="selector" value="paired"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
888 <param name="subsampling_paired" value="20257"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
889 <param name="subsampling_seed" value="42"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
890 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
891 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
892 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
893 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
894 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
895 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
896 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
897 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
898 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
899 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
900 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
901 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
902 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
903 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
904 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
905 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
906 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
907 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
908 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
909 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
910 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
911 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
912 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
913 <output_collection name="subsample_paired" type="paired">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
914 <element name="forward">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
915 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
916 <has_line_matching expression="^@.*" n="10128"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
917 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
918 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
919 <element name="reverse">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
920 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
921 <has_line_matching expression="^@.*" n="10128"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
922 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
923 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
924 </output_collection>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
925 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
926 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
927 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
928 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
929 <!-- Paired fastq file as collection, Cached db -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
930 <test expect_num_outputs="4">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
931 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
932 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
933 <param name="selector" value="raw"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
934 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
935 <param name="selector" value="paired_collection"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
936 <param name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
937 <collection type="paired" name="pair">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
938 <element name="forward" value="SRS014464-Anterior_nares_mini.fastq" />
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
939 <element name="reverse" value="SRS014464-Anterior_nares_mini.fastq" />
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
940 </collection>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
941 </param>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
942 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
943 <param name="read_min_len" value="70"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
944 <section name="mapping">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
945 <param name="bt2_ps" value="sensitive"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
946 <param name="min_mapq_val" value="5"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
947 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
948 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
949 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
950 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
951 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
952 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
953 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
954 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
955 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
956 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
957 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
958 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
959 <param name="split_levels" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
960 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
961 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
962 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
963 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
964 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
965 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
966 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
967 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
968 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
969 <conditional name="subsample">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
970 <param name="selector" value="no"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
971 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
972 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
973 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
974 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
975 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
976 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
977 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
978 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
979 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
980 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
981 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
982 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
983 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
984 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
985 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
986 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
987 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
988 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
989 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
990 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
991 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
992 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
993 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
994 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
995 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
996 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
997 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
998 <!-- SAM, cached DB -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
999 <test expect_num_outputs="2">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1000 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1001 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1002 <param name="selector" value="sam"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1003 <param name="in" value="SRS014464-Anterior_nares.sam"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1004 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1005 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1006 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1007 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1008 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1009 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1010 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1011 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1012 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1013 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1014 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1015 <param name="split_levels" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1016 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1017 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1018 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1019 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1020 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1021 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1022 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1023 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1024 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1025 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1026 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1027 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1028 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1029 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1030 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1031 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1032 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1033 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1034 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1035 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1036 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1037 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1038 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1039 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1040 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1041 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1042 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1043 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1044 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1045 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1046 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1047 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1048 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1049 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1050 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1051 <!-- bowtie2out, cached DB -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1052 <test expect_num_outputs="2">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1053 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1054 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1055 <param name="selector" value="bowtie2out"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1056 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1057 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1058 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1059 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1060 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1061 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1062 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1063 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1064 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1065 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1066 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1067 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1068 <param name="split_levels" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1069 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1070 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1071 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1072 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1073 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1074 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1075 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1076 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1077 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1078 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1079 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1080 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1081 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1082 <param name="legacy_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1083 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1084 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1085 <param name="krona_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1086 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1087 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1088 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1089 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1090 <has_text text="relative_abundance"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1091 <has_text text="NCBI_tax_id"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1092 <has_text text="clade_name"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1093 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1094 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1095 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1096 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1097 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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diff changeset
1098 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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diff changeset
1099 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1100 <assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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1101 <has_text text="Downloading" negate="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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1102 </assert_stderr>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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1103 </test>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1104 <!-- Single FASTA file, Cached db -->
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1105 <test expect_num_outputs="6">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1106 <section name="inputs">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1107 <conditional name="in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1108 <param name="selector" value="raw"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1109 <conditional name="raw_in">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1110 <param name="selector" value="single"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1111 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1112 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1113 <param name="read_min_len" value="70"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1114 <section name="mapping">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1115 <param name="bt2_ps" value="sensitive"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1116 <param name="min_mapq_val" value="5"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1117 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1118 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1119 <conditional name="db">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1120 <param name="db_selector" value="cached"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1121 <param name="cached_db" value="test-db-20210409"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1122 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1123 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1124 <section name="analysis">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1125 <conditional name="analysis_type">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1126 <param name="t" value="rel_ab"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1127 <conditional name="tax_lev">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1128 <param name="tax_lev" value="a"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1129 <param name="split_levels" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1130 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1131 </conditional>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1132 <param name="min_cu_len" value="2000"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1133 <param name="organism_profiling" value="add_viruses"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1134 <param name="stat" value="avg_g"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1135 <param name="stat_q" value="0.2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1136 <param name="perc_nonzero" value="0.33"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1137 <param name="ignore_markers" value="marker.txt"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1138 <param name="avoid_disqm" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1139 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1140 <section name="out">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1141 <param name="sample_id_key" value="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1142 <param name="sample_id" value="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1143 <param name="use_group_representative" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1144 <param name="legacy_output" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1145 <param name="CAMI_format_output" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1146 <param name="unclassified_estimation" value="false"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1147 <param name="krona_output" value="true"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1148 </section>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1149 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1150 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1151 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1152 <has_text text="SampleID"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1153 <has_text text="Metaphlan_Analysis"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1154 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1155 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1156 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1157 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1158 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1159 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1160 </output>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1161 <output_collection name="levels" type="list">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1162 <element name="all" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1163 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1164 <has_text text="Gammaproteobacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1165 <has_text text="Corynebacterium accolens"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1166 <has_n_columns n="9"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1167 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1168 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1169 <element name="class" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1170 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1171 <has_text text="class"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1172 <has_text text="Actinobacteria"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1173 <has_n_columns n="2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1174 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1175 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1176 <element name="family" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1177 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1178 <has_text text="family"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1179 <has_text text="Propionibacteriaceae"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1180 <has_n_columns n="2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1181 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1182 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1183 <element name="genus" ftype="tabular">
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1184 <assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1185 <has_text text="genus"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1186 <has_text text="Cutibacterium"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
estrain
parents:
diff changeset
1187 <has_n_columns n="2"/>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1188 </assert_contents>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
diff changeset
1189 </element>
a7bd05df0bea planemo upload commit e485da3e1b9eb674a52948a00a3328c1a3cc5ffa
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parents:
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1190 <element name="kingdom" ftype="tabular">
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1191 <assert_contents>
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1192 <has_text text="kingdom"/>
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1193 <has_text text="Bacteria"/>
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1194 <has_n_columns n="2"/>
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1195 </assert_contents>
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1196 </element>
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1197 <element name="order" ftype="tabular">
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1198 <assert_contents>
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1199 <has_text text="order"/>
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1200 <has_text text="Propionibacteriales"/>
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1201 <has_n_columns n="2"/>
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1202 </assert_contents>
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1203 </element>
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1204 <element name="phylum" ftype="tabular">
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1205 <assert_contents>
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1206 <has_text text="phylum"/>
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1207 <has_text text="Firmicutes"/>
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1208 <has_n_columns n="2"/>
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1209 </assert_contents>
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1210 </element>
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1211 <element name="species" ftype="tabular">
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1212 <assert_contents>
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1213 <has_text text="species"/>
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1214 <has_text text="Corynebacterium accolens"/>
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1215 <has_n_columns n="2"/>
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1216 </assert_contents>
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1217 </element>
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1218 <element name="strains" ftype="tabular">
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1219 <assert_contents>
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1220 <has_text text="strains"/>
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1221 <has_n_columns n="2"/>
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1222 </assert_contents>
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1223 </element>
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1224 </output_collection>
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1225 <output name="krona_output_file" ftype="tabular">
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1226 <assert_contents>
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1227 <not_has_text text="k__Bacteria"/>
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1228 <has_text text="Corynebacterium accolens"/>
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1229 <has_n_columns n="9"/>
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1230 </assert_contents>
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1231 </output>
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1232 <assert_stderr>
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1233 <has_text text="Downloading" negate="true"/>
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1234 </assert_stderr>
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1235 </test>
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1236 <!-- Check a non-default analysis mode
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1237 and viral analysis -->
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1238 <test expect_num_outputs="6">
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1239 <section name="inputs">
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1240 <conditional name="in">
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1241 <param name="selector" value="raw"/>
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1242 <conditional name="raw_in">
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1243 <param name="selector" value="single"/>
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1244 <param name="in" value="SRS014464-Anterior_nares.fastq.gz"/>
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1245 </conditional>
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1246 </conditional>
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1247 <conditional name="db">
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1248 <param name="db_selector" value="cached"/>
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1249 <param name="cached_db" value="mpa_vJan21_TOY_CHOCOPhlAnSGB"/>
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1250 </conditional>
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1251 </section>
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1252 <section name="analysis">
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1253 <conditional name="analysis_type">
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1254 <param name="t" value="marker_ab_table"/>
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1255 </conditional>
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1256 </section>
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1257 <conditional name="viral_analysis">
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1258 <param name="profile_vsc" value="--profile_vsc"/>
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1259 </conditional>
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1260 <conditional name="subsample">
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1261 <param name="selector" value="single"/>
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1262 <param name="subsampling" value="10000"/>
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1263 <param name="subsampling_seed" value="42"/>
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1264 </conditional>
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1265 <param name="test" value="true"/>
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1266 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
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diff changeset
1267 <assert_contents>
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1268 <has_text text="SGB7017__MKDPKOFL_00679"/>
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1269 <has_text text="SampleID"/>
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1270 <has_text text="Metaphlan_Analysis"/>
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1271 </assert_contents>
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1272 </output>
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1273 <output name="subsample_single">
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1274 <assert_contents>
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1275 <has_text text="@" n="10000"/>
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1276 </assert_contents>
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1277 </output>
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1278 <!-- reference data empty -> empty output -->
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diff changeset
1279 <output name="vcs_breath_coverage" ftype="tabular">
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diff changeset
1280 <assert_contents>
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1281 <has_size size="0"/>
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1282 </assert_contents>
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1283 </output>
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1284 <assert_command>
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1285 <has_text text="--profile_vsc"/>
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1286 <has_text text="--vsc_breadth 0.75"/>
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1287 <has_text text="--vsc_out"/>
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1288 </assert_command>
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1289 <assert_stderr>
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1290 <has_text text="Downloading"/>
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1291 <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->
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1292 <has_text text="No reads aligning to VSC markers"/>
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1293 </assert_stderr>
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1294 </test>
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1295 </tests>
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1296 <help><![CDATA[
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1297 What it does
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1298 ============
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1299
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1300 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
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1301 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.
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1302
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1303 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes
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1304 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
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1305
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1306 - unambiguous taxonomic assignments;
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1307 - accurate estimation of organismal relative abundance;
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1308 - species-level resolution for bacteria, archaea, eukaryotes and viruses;
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1309 - strain identification and tracking
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1310 - orders of magnitude speedups compared to existing methods.
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1311 - microbiota strain-level population genomics
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diff changeset
1312
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1313 MetaPhlAn clade-abundance estimation
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1314 ------------------------------------
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1315
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1316 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and
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1317 strains in particular cases) present in the microbiota obtained from a microbiome sample and their
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1318 relative abundance.
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1319
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1320 Marker level analysis
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1321 ---------------------
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1322
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1323 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non
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1324 aggregated marker information. Such capability comes with several slightly different flavours and
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1325 are a way to perform strain tracking and comparison across multiple samples.
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1326
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1327 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
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1328 species present in the community, and then a strain-level profiling can be performed to zoom-in on
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1329 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out
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1330 intermediate file saved during the execution of the default analysis type.
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1331
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1332 Inputs
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1333 ======
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1334
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1335 Metaphlan takes as input either:
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1336
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1337 - one or several sequence files in Fasta, FastQ (whether compressed or not)
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1338 - a BowTie2 produced SAM file
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1339 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run
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1340
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1341 It also needs the reference database, which can be locally installed or customized using the dedicated tools.
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1342
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1343 Outputs
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1344 =======
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1345
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1346 The main output is a tab-separated file with the predicted taxon relative abundances.
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1347
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1348 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.
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1349
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1350
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1351 More help and use cases
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1352 =======================
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1353
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1354 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.
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1355
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1356 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage
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1357
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1358 ]]></help>
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1359 <expand macro="citations"/>
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1360 </tool>