Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.xml @ 17:8c6ee1c2248f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"
author artbio
date Tue, 05 Oct 2021 22:28:34 +0000
parents 31e7a33ecd71
children 8d9f31389f33
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16:31e7a33ecd71 17:8c6ee1c2248f
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy1"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy2">
2 <description>from genomic variations in vcf files</description> 2 <description>from genomic variations in vcf files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> 4 <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
5 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement> 5 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
6 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement> 6 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
23 </stdio> 23 </stdio>
24 24
25 <command detect_errors="exit_code"><![CDATA[ 25 <command detect_errors="exit_code"><![CDATA[
26 #import json 26 #import json
27 #import os 27 #import os
28 Rscript $__tool_directory__/mutational_patterns.R 28 Rscript $__tool_directory__/mutational_patterns.R
29 --inputs 29 --inputs
30 #set $filename_to_element_identifiers = {} 30 #set $filename_to_element_identifiers = {}
31 #for $sample in $vcfs: 31 #for $sample in $vcfs:
32 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier) 32 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
33 #end for 33 #end for
60 #end if 60 #end if
61 61
62 #if $rdata_out 62 #if $rdata_out
63 --rdata '$rdata' 63 --rdata '$rdata'
64 #end if 64 #end if
65
66 --tooldir '$__tool_directory__/'
65 67
66 ]]></command> 68 ]]></command>
67 <inputs> 69 <inputs>
68 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> 70 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
69 <param name="genome" type="select" label="Reference Genome"> 71 <param name="genome" type="select" label="Reference Genome">
133 label="selects the N most significant signatures in samples to express mutational patterns" 135 label="selects the N most significant signatures in samples to express mutational patterns"
134 help="an integer between 2 and 30 signature types from cosmic"/> 136 help="an integer between 2 and 30 signature types from cosmic"/>
135 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set"> 137 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
136 <option value="v2" selected="true">Cosmic v2, March 2015</option> 138 <option value="v2" selected="true">Cosmic v2, March 2015</option>
137 <option value="v3">Cosmic v3, May 2019</option> 139 <option value="v3">Cosmic v3, May 2019</option>
140 <option value="v3.1">Cosmic v3.1, June 2020</option>
141 <option value="v3.2">Cosmic v3.2, March 2021</option>
138 </param> 142 </param>
139 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" 143 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
140 help="Output the normalized signatures contributions for further visualization" > 144 help="Output the normalized signatures contributions for further visualization" >
141 <option value="no" selected="true">No</option> 145 <option value="no" selected="true">No</option>
142 <option value="yes">Yes</option> 146 <option value="yes">Yes</option>