comparison mutational_patterns.xml @ 3:843f654e1752 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"

2:42ea09d3e693

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy1">
    <description>from genomic variations in vcf files</description>
    <requirements>
        <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
        <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
        <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>

    </stdio>

    <command detect_errors="exit_code"><![CDATA[
#import json
#import os
Rscript $__tool_directory__/mutational_patterns.R 
    --inputs
    #set $filename_to_element_identifiers = {}
    #for $sample in $vcfs:
        $filename_to_element_identifiers.__setitem__(str($sample),  $sample.element_identifier)
    #end for

    #end if
            
    #if $rdata_out
        --rdata '$rdata'
    #end if

]]></command>
    <inputs>
        <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
        <param name="genome" type="select" label="Reference Genome">

                       label="selects the N most significant signatures in samples to express mutational patterns"
                       help="an integer between 2 and 30 signature types from cosmic"/>
                <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
                    <option value="v2" selected="true">Cosmic v2, March 2015</option>
                    <option value="v3">Cosmic v3, May 2019</option>
                </param>
                <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
                       help="Output the normalized signatures contributions for further visualization" >
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>

3:843f654e1752

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy2">
    <description>from genomic variations in vcf files</description>
    <requirements>
        <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
        <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
        <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>

    </stdio>

    <command detect_errors="exit_code"><![CDATA[
#import json
#import os
Rscript $__tool_directory__/mutational_patterns.R
    --inputs
    #set $filename_to_element_identifiers = {}
    #for $sample in $vcfs:
        $filename_to_element_identifiers.__setitem__(str($sample),  $sample.element_identifier)
    #end for

    #end if
            
    #if $rdata_out
        --rdata '$rdata'
    #end if
    
    --tooldir '$__tool_directory__/'

]]></command>
    <inputs>
        <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
        <param name="genome" type="select" label="Reference Genome">

                       label="selects the N most significant signatures in samples to express mutational patterns"
                       help="an integer between 2 and 30 signature types from cosmic"/>
                <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
                    <option value="v2" selected="true">Cosmic v2, March 2015</option>
                    <option value="v3">Cosmic v3, May 2019</option>
                    <option value="v3.1">Cosmic v3.1, June 2020</option>
                    <option value="v3.2">Cosmic v3.2, March 2021</option>
                </param>
                <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
                       help="Output the normalized signatures contributions for further visualization" >
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>