comparison mutational_patterns.xml @ 23:83f8c93c34b4 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"

22:00be8f0b2c89

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy7">
    <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="1.1.1l=h7f98852_0">openssl</requirement>
        <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement>

            --own_signatures '$set_preset.set_signature_input.own_matrix'
        #end if
       
        --signum '$set_preset.signum'
        --colors '$set_preset.colors'
        --output_sigpattern '$sig_contrib'

        #if $set_preset.contrib_matrix_out == 'yes'
            --sig_contrib_matrix '$sig_contrib_matrix'
        #end if

                    </when>
                </conditional>
                <param name="signum" type="integer" value="3" min="2" max="30"
                       label="selects the N most significant signatures in samples to express mutational patterns"
                       help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
                <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>
                </param>
                <param name="colors" type="select" label="Color set" display="radio">

            <filter>rdata_out</filter>
        </data>

    </outputs>
    <tests>
         <!-- user defined (v3.2 restricted 30 minus 27) -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>
                    <element name="7" value="G.vcf"/>

                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="cosmic" />
                    <param name="cosmic_version" value="v3.2"/>
                </conditional>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="3" />
            <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>

23:83f8c93c34b4

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy8">
    <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="1.1.1l=h7f98852_0">openssl</requirement>
        <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement>

            --own_signatures '$set_preset.set_signature_input.own_matrix'
        #end if
       
        --signum '$set_preset.signum'
        --colors '$set_preset.colors'
        --display_signatures '$set_preset.display_signatures'
        --output_sigpattern '$sig_contrib'

        #if $set_preset.contrib_matrix_out == 'yes'
            --sig_contrib_matrix '$sig_contrib_matrix'
        #end if

                    </when>
                </conditional>
                <param name="signum" type="integer" value="3" min="2" max="30"
                       label="selects the N most significant signatures in samples to express mutational patterns"
                       help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
                <param name="display_signatures" type="select" display="radio" label="Output profiles of input signatures ?">
                    <option value="no">No</option>
                    <option value="yes" selected="true">Yes</option>
                </param>
                <param name="contrib_matrix_out" type="select" display="radio" 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>
                </param>
                <param name="colors" type="select" label="Color set" display="radio">

            <filter>rdata_out</filter>
        </data>

    </outputs>
    <tests>
         <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>
                    <element name="7" value="G.vcf"/>

                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="cosmic" />
                    <param name="cosmic_version" value="v3.2"/>
                </conditional>
                <param name="display_signatures"  value="no" />
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="3" />
            <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>