Mercurial > repos > iuc > colibread_commet

comparison commet.xml @ 5:701b1ab185fe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:40:30 +0000
parents 0b9a713ece1d
children 5918765a6426
comparison
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4:a4d4b2564a2a 5:701b1ab185fe
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@">
2 <tool profile="16.04" id="commet" name="Commet" version="24.7.14">
3 <description>COmpare Multiple METagenomes</description> 2 <description>COmpare Multiple METagenomes</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <requirements> 6 <requirements>
8 <requirement type="package" version="24.7.14">commet</requirement> 7 <requirement type="package" version="24.7.14">commet</requirement>
9 </requirements> 8 </requirements>
10 <command><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 #for $i, $set in enumerate( $sets ) 10 #for $i, $set in enumerate($sets):
12 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt && 11 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
13 #end for 12 #end for
14 Commet.py 13 Commet.py
15 -k ${k} 14 -k ${k}
16 -t ${t} 15 -t ${t}
17 -l ${l} 16 -l ${l}
18 -e ${e} 17 -e ${e}
19 #if str( $options_advanced.options_advanced_selector ) == "advanced" 18 #if str($options_advanced.options_advanced_selector) == "advanced":
20 -m ${options_advanced.m} 19 -m ${options_advanced.m}
21 -n ${options_advanced.n} 20 -n ${options_advanced.n}
22 #end if 21 #end if
23 commet_input_sets.txt 22 commet_input_sets.txt
24
25 ]]></command> 23 ]]></command>
26
27 <inputs> 24 <inputs>
28 <!-- Input data files -->
29 <repeat name="sets" title="Read sets" min="1"> 25 <repeat name="sets" title="Read sets" min="1">
30 <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/> 26 <param name="reads" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="Dataset" help="Accept fasta/fastq"/>
31 </repeat> 27 </repeat>
32 <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." /> 28 <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
33 <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." /> 29 <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
34 <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." /> 30 <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
35 <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." /> 31 <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />
71 </outputs> 67 </outputs>
72 <tests> 68 <tests>
73 <test> 69 <test>
74 <param name="input_type" value="list" /> 70 <param name="input_type" value="list" />
75 <repeat name="sets"> 71 <repeat name="sets">
76 <param name="reads" value="commet/A.fa" ftype="fasta" /> 72 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
77 </repeat> 73 </repeat>
78 <repeat name="sets"> 74 <repeat name="sets">
79 <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" /> 75 <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" />
80 </repeat> 76 </repeat>
81 <repeat name="sets"> 77 <repeat name="sets">
82 <param name="reads" value="commet/D.fa" ftype="fasta" /> 78 <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" />
83 </repeat> 79 </repeat>
84 <param name="plain_outputs" value="True"/> 80 <param name="plain_outputs" value="True"/>
85 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/> 81 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
86 <output name="matrix_plain" file="commet/matrix_plain.csv"/> 82 <output name="matrix_plain" file="commet/matrix_plain.csv"/>
87 </test> 83 </test>