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1 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
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2 <description>to index, or lookup cached alignment</description>
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3 <requirements>
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4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
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5 <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
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6 <requirement type="package" version="2.4.5">bowtie2</requirement>
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7 <requirement type="package" version="1.9.134">boto3</requirement> -->
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8 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
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12 #if $reads.reads_select == 'collection'
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13 #set forward=$reads.coll.forward
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14 #set reverse=$reads.coll.reverse
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15 #end if
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16 python ${__tool_directory__}/snp-cache.py snp_mapped_reads
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17 "\$(md5sum $reference
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18 $forward
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19 $reverse
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20 | cut -c -32 | md5sum | cut -c -32)"
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21 -c "
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22 cp $reference ./reference.fasta
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23 #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
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24 && cp $forward ./forward.gz
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25 #set $forward="./forward.gz"
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26 #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
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27 && cp $forward ./forward.bz2
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28 #set $forward="./forward.bz2"
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29 #end if
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30 #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
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31 && cp $reverse ./reverse.gz
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32 #set $reverse="./reverse.gz"
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33 #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
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34 && cp $reverse ./reverse.bz2
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35 #set $reverse="./reverse.bz2"
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36 #end if
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37 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
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38 && bowtie2 -q -x ./reference -1 $forward -2 $reverse -p \${GALAXY_SLOTS:-4} --reorder -X 1000
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39 "
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40 #if $reads.reads_select == 'collection'
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41 -o ${align_from_collection}
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42 #else
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43 -o ${align_from_history}
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44 #end if
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45 -l $cache_log
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46 && cat $cache_log
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47 #if $source.source_select == 'curated'
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48 && cp $reference $ref_out
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49 #end if
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50 ]]></command>
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51 <inputs>
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52 <!-- <conditional name="source">
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53 <param name="source_select" type="select" label="Use the reference associated with a provided BioProject, a curated GalaxyTrakr reference, or a reference from your history">
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54 <option value="bioproject">Provide a BioProject</option>
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55 <option value="curated">Use a GalaxyTrakr reference</option>
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56 <option value="history">Use a reference from your history</option>
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57 </param>
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58 <when value="bioproject">
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59 <param type="data" name="bioproject" format="text" />
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60 </when>
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61 <when value="curated">
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62 <param name="input" type="select" label="Select reference fasta">
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63 <options from_data_table="all_fasta">
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64 <filter type="sort_by" column="2"/>
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65 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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66 </options>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
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71 </when>
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72 </conditional> -->
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73 <conditional name="source">
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74 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
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75 <option value="curated">Use a GalaxyTrakr reference</option>
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76 <option value="history">Use a reference from your history</option>
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77 </param>
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78 <when value="curated">
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79 <param name="reference" type="select" label="Select reference fasta">
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80 <options from_data_table="all_fasta">
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81 <filter type="sort_by" column="2"/>
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82 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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83 </options>
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84 </param>
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85 </when>
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86 <when value="history">
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87 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
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88 </when>
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89 </conditional>
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90 <conditional name="reads">
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91 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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92 <option value="collection">Paired collection from your history</option>
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93 <option value="history">Two FASTQ datasets from your history</option>
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94 </param>
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95 <when value="collection">
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96 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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97 </when>
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98 <when value="history">
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99 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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100 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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101 </when>
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102 </conditional>
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103 </inputs>
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104 <outputs>
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105 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
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106 <filter>reads['reads_select'] == 'collection'</filter>
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107 </data>
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108 <data label="${reads.forward.name.split('_')[0]} alignment" name="align_from_history" format="sam">
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109 <filter>reads['reads_select'] == 'history'</filter>
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110 </data>
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111 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
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112 <data label="Reference" name="ref_out" format="fasta" hidden="true">
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113 <filter>source['source_select'] == curated</filter>
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114 </data>
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115 </outputs>
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116 <tests>
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117 <test>
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118 <param name="source_select" value="history" />
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119 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
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120 <param name="reads_select" value="history" />
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121 <param name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
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122 <param name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
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123 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
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124 </test>
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125 <test>
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126 <param name="source_select" value="history" />
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127 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
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128 <param name="reads_select" value="collection" />
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129 <param name="coll">
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130 <collection type="paired">
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131 <element name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
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132 <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
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133 </collection>
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134 </param>
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135 <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
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136 </test>
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137 <test>
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138 <param name="source_select" value="history" />
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139 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
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140 <param name="reads_select" value="history" />
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141 <param name="forward" value="samples/sample1/sample1_1.fastq.gz" ftype="fastqsanger.gz" />
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142 <param name="reverse" value="samples/sample1/sample1_2.fastq.gz" ftype="fastqsanger.gz" />
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143 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
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144 </test>
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145 </tests>
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146 <help><![CDATA[
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147 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
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148 ]]></help>
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149 <citations>
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150 <citation type="doi">10.7717/peerj-cs.20</citation>
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151 <!-- <citation type="bibtex">
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152 @misc{cfsan-snp-pipeline,
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153 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
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154 year = {2015},
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155 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
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156 url = {https://doi.org/10.7717/peerj-cs.20},
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157 journal = {PeerJ Computer Science},
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158 }</citation> -->
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159 </citations>
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160 </tool> |
