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planemo upload commit 41caf97a4a9a7928318af8b24601f84a380fe2db
author galaxytrakr
date Fri, 18 Sep 2026 12:26:54 +0000
parents 56b71adcaba7
children
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1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.24" profile="21.05">
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2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description>
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3 <requirements>
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4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container>
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5 </requirements>
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6
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9 #def fix_ext($ext):
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10 #set ext = $ext.replace('fastqsanger', 'fastq')
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11 #set ext = $ext.replace('fastqillumina', 'fastq')
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12 #return $ext
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13 #end def
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14
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15 mkdir -p ./mitochondria7 ./jobs7m &&
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17 ## ── Link database files into working directory ────────────────────────
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18 ln -sf '${probe_db.fields.path}'/* ./mitochondria7/ &&
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20 ## ── Symlink kmerread7 binary into working directory ───────────────────
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21 ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
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22
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23 ## ── Stage input reads and build jobs file ────────────────────────────
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24 #if $reads.reads_type == "single_file"
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25 mkdir -p ./reads &&
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26 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
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27 #set ext = $fix_ext($reads.input.ext)
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28 #set fname = re.sub('[^\w\-_.]', '_', $reads.input.element_identifier) + '.' + $ext
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29 ln -sf '$reads.input' './reads/${fname}' &&
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30 printf '%s\t1\n' '${sample_name}' > ./jobs7m/jobs7m.txt &&
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31 printf '%s\n' './reads/${fname}' >> ./jobs7m/jobs7m.txt &&
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32 #else if $reads.reads_type == "single"
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33 mkdir -p ./reads &&
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34 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
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35 #set read_count = 0
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36 #for $read in $reads.input
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37 #set ext = $fix_ext($read.ext)
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38 #set fname = re.sub('[^\w\-_.]', '_', $read.element_identifier) + '.' + $ext
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39 ln -sf '$read' './reads/${fname}' &&
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40 #set read_count = $read_count + 1
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41 #end for
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42 printf '%s\t%d\n' '${sample_name}' ${read_count} > ./jobs7m/jobs7m.txt &&
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43 #for $read in $reads.input
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44 #set ext = $fix_ext($read.ext)
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45 #set fname = re.sub('[^\w\-_.]', '_', $read.element_identifier) + '.' + $ext
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46 printf '%s\n' './reads/${fname}' >> ./jobs7m/jobs7m.txt &&
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47 #end for
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48 #else
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49 ## paired collection: forward + reverse
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50 mkdir -p ./reads &&
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51 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
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52 #set fwd_ext = $fix_ext($reads.input.forward.ext)
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53 #set rev_ext = $fix_ext($reads.input.reverse.ext)
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54 #set base = re.sub('[^\w\-_.]', '_', $reads.input.element_identifier)
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55 #set fwd_fname = $base + '_1.' + $fwd_ext
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56 #set rev_fname = $base + '_2.' + $rev_ext
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57 ln -sf '$reads.input.forward' './reads/${fwd_fname}' &&
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58 ln -sf '$reads.input.reverse' './reads/${rev_fname}' &&
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59 printf '%s\t2\n' '${sample_name}' > ./jobs7m/jobs7m.txt &&
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60 printf '%s\n' './reads/${fwd_fname}' >> ./jobs7m/jobs7m.txt &&
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61 printf '%s\n' './reads/${rev_fname}' >> ./jobs7m/jobs7m.txt &&
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62 #end if
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63
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64 ## ── Run the Python orchestrator ───────────────────────────────────────
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65 python3 /opt/mitokmer2/kmer_read_m7.py &&
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66
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67 ## ── Copy output CSV to Galaxy output path ─────────────────────────────
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68 cp ./jobs7m/jobs7m.csv '${results_csv}'
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69 ]]></command>
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70
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71 <inputs>
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72 <param name="probe_db" type="select" label="Mitochondrial k-mer probe database"
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73 help="Select a pre-installed mitochondrial k-mer probe database.
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74 Databases are managed by your Galaxy administrator via the
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75 mitokmer_probe_db data table.">
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76 <options from_data_table="mitokmer_probe_db">
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77 <filter type="sort_by" column="1" />
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78 <validator type="no_options" message="No mitochondrial k-mer probe databases are
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79 currently installed. Please contact your Galaxy administrator." />
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80 </options>
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81 </param>
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82
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83 <conditional name="reads">
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84 <param name="reads_type" type="select" label="Input read type">
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85 <option value="single_file">Single FASTA or FASTQ dataset</option>
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86 <option value="single">Single-end or unpaired reads / FASTA (list collection)</option>
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87 <option value="paired">Paired-end reads (paired collection)</option>
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88 </param>
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89 <when value="single_file">
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90 <param name="input" type="data"
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91 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fasta,fasta.gz"
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92 label="Input FASTA or FASTQ dataset"
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93 help="Provide a single FASTA or FASTQ file from your history." />
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94 </when>
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95 <when value="single">
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96 <param name="input" type="data_collection" collection_type="list"
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97 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fasta,fasta.gz"
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98 label="Input reads (FASTQ or FASTA, gzipped or plain)"
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99 help="Provide one or more single-end or unpaired read files as a Galaxy
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100 list collection. For paired-end data, use the 'Paired-end reads'
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101 option instead." />
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102 </when>
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103 <when value="paired">
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104 <param name="input" type="data_collection" collection_type="paired"
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105 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz"
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106 label="Paired-end reads (paired collection)"
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107 help="Provide a Galaxy paired collection containing forward (R1) and
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108 reverse (R2) reads. Light quality trimming of read ends is
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109 performed internally; pre-trimming is optional." />
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110 </when>
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111 </conditional>
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112 </inputs>
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113
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114 <outputs>
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115 <data name="results_csv" format="csv" label="mitoKmer results for ${on_string}" />
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116 </outputs>
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117
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118 <tests>
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119 <!-- Test 1: single FASTA dataset -->
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120 <test>
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121 <param name="probe_db" value="mitoch_probes_sample" />
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122 <conditional name="reads">
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123 <param name="reads_type" value="single_file" />
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124 <param name="input" value="test/Plodia_assembly.fasta" ftype="fasta" />
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125 </conditional>
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126 <output name="results_csv">
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127 <assert_contents>
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128 <has_text text="Plodia" />
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <!-- Test 2: paired-end FASTQ via paired collection -->
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133 <test>
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134 <param name="probe_db" value="mitoch_probes_sample" />
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135 <conditional name="reads">
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136 <param name="reads_type" value="paired" />
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137 <param name="input">
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138 <collection type="paired">
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139 <element name="forward" value="test/Plodia_R1.fastq.gz" ftype="fastqsanger.gz" />
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140 <element name="reverse" value="test/Plodia_R2.fastq.gz" ftype="fastqsanger.gz" />
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141 </collection>
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142 </param>
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143 </conditional>
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144 <output name="results_csv">
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145 <assert_contents>
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146 <has_text text="Plodia" />
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147 </assert_contents>
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148 </output>
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149 </test>
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150 <!-- Test 3: single-end FASTQ via list collection -->
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151 <test>
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152 <param name="probe_db" value="mitoch_probes_sample" />
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153 <conditional name="reads">
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154 <param name="reads_type" value="single" />
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155 <param name="input">
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156 <collection type="list">
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157 <element name="Plodia_R1" value="test/Plodia_R1.fastq.gz" ftype="fastqsanger.gz" />
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158 </collection>
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159 </param>
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160 </conditional>
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161 <output name="results_csv">
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162 <assert_contents>
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163 <has_text text="Plodia" />
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164 </assert_contents>
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165 </output>
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166 </test>
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167 <!-- Test 4: FASTA list collection -->
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168 <test>
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169 <param name="probe_db" value="mitoch_probes_sample" />
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170 <conditional name="reads">
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171 <param name="reads_type" value="single" />
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172 <param name="input">
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173 <collection type="list">
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174 <element name="Plodia_assembly" value="test/Plodia_assembly.fasta" ftype="fasta" />
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175 </collection>
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176 </param>
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177 </conditional>
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178 <output name="results_csv">
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179 <assert_contents>
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180 <has_text text="Plodia" />
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181 </assert_contents>
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182 </output>
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183 </test>
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184 </tests>
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185
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186 <help><![CDATA[
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187 **mitoKmer** — Metagenomic Mitochondrial Read Identification by K-mer Database
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188 ===============================================================================
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189
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190 Overview
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191 --------
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192 mitoKmer identifies the taxonomic origin of short-read shotgun sequencing data
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193 by matching reads against a database of species-specific mitochondrial k-mer
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194 probes. It reports the relative abundance of taxa at multiple taxonomic ranks
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195 (e.g. order, species) along with the number of matching reads and supporting
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196 unique k-mers.
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197
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198 Inputs
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199 ------
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200 **Mitochondrial k-mer probe database**
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201 Select a pre-installed probe database from the dropdown. Databases are
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202 managed by your Galaxy administrator and registered in the
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203 ``mitokmer_probe_db`` data table. The database consists of a directory
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204 of ``.txt`` files.
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205
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206 **Input read type**
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207 Choose the input mode that matches your data:
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208
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209 *Single FASTA or FASTQ dataset*
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210 Provide a single FASTA or FASTQ file directly from your history.
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211 This is the simplest option for a single assembled sequence or
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212 single-end read file.
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213
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214 *Single-end or unpaired reads / FASTA (list collection)*
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215 Provide a Galaxy **list** collection containing one or more FASTQ
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216 (``fastqsanger``, ``fastqsanger.gz``) or FASTA (``fasta``,
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217 ``fasta.gz``) files. Use this for single-end sequencing data or
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218 multiple assembled FASTA sequences processed together.
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219
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220 *Paired-end reads (paired collection)*
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221 Provide a Galaxy **paired** collection where the forward (R1) and
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222 reverse (R2) reads are paired together. Both files must be FASTQ
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223 format (``fastqsanger`` or ``fastqsanger.gz``).
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224
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225 In all cases, light window-based quality trimming of read ends is
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226 performed internally; pre-trimming is optional.
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227
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228 Output
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229 ------
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230 **Results CSV**
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231 A comma-separated file with one row per taxon detected. Columns:
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232
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233 ========= ============================================================
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234 Column Description
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235 ========= ============================================================
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236 Rank Taxonomic rank (e.g. Order, Species)
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237 Taxon Taxon name
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238 Reads Number of reads matching this taxon
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239 Rel_Abund Relative abundance (%)
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240 Unique_kmers Number of unique k-mers supporting the match
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241 ========= ============================================================
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242
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243 Only taxa with non-zero relative abundance are reported.
0
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244
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245 Example output for the "Plodia" test sample::
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246
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247 Rank Taxon Reads Rel_Abund(%) Unique_kmers
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248 Order Lepidoptera 10 0.1 329
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249 Species Plodia interpunctella 462 99.9 466
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250
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251 Citation
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252 --------
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253 Please cite the mitoKmer GitHub repository if you use this tool in published work.
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254 ]]></help>
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255
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256 <citations>
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257 <citation type="bibtex">
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258 @misc{githubmitokmer2,
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259 author = {Mammel, Mark},
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260 title = {mitoKmer2},
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261 year = {2024},
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262 publisher = {GitHub},
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263 journal = {GitHub repository},
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264 url = {https://github.com/mmammel8/mitokmer2},
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265 }
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266 </citation>
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267 </citations>
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268 </tool>