comparison mutational_patterns.xml @ 1:c73aa7cc4c4b draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"

0:d585f369bfad

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14">
    <description>from genomic variations in vcf files</description>
    <requirements>
        <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
        <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
        <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
        <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
        <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
<!--
        <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
        <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
-->
<!--

    #if $set_cosmic.choices == 'yes':
        --cosmic_version '$set_cosmic.cosmic_version'
        --signum '$set_cosmic.signum'
        --output_cosmic $cosmic
        #if $set_cosmic.contrib_matrix_out
            --sig_contrib_matrix $sig_contrib_matrix
        #end if
    #end if
            
    #if $rdata_out

            </when>
            <when value="no" />
        </conditional>

        <conditional name="set_cosmic">
            <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param name="signum" type="integer" value="3" min="2" max="30"

                       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="boolean" checked="false" label="Output Signature Contribution table ?"
                       help="Output the normalized signatures contributions for further visualization" />
            </when>
             <when value="no" />
        </conditional>
        <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
    </inputs>

        </data>
        <data name="cosmic" format="pdf" label="Cosmic signatures">
            <filter>set_cosmic['choices'] == "yes"</filter>
        </data>
        <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
            <filter>set_cosmic['contrib_matrix_out']</filter>
        </data>

        <data name="rdata" format="rdata" label="${tool.name}: RData file">
            <filter>rdata_out</filter>
        </data>

    </outputs>
    <tests>
        <!-- simple profile -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" ftype="vcf" value="G.vcf"/>

            <param name="rdata_out" value="true" />
            <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
            <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
        </test>

         <!-- cosmic signatures -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>
                    <element name="7" value="G.vcf"/>
                    <element name="8" value="H.vcf"/>
                    <element name="9" value="I.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
            <conditional name="set_spectrum">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="yes"/>
                <param name="contrib_matrix_out"  value="true" />
            </conditional>
            <param name="signum" value="3" />
            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
        </test>
        <!-- cosmic signature on single sample -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" value="G.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <conditional name="set_spectrum">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="yes"/>
            </conditional>
            <param name="signum" value="5" />
            <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
        </test>
    </tests>
    <help>

**What it does**

1:c73aa7cc4c4b

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0">
    <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>
        <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
        <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
<!--
        <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
        <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
-->
<!--

    #if $set_cosmic.choices == 'yes':
        --cosmic_version '$set_cosmic.cosmic_version'
        --signum '$set_cosmic.signum'
        --output_cosmic $cosmic
        #if $set_cosmic.contrib_matrix_out == 'yes'
            --sig_contrib_matrix $sig_contrib_matrix
        #end if
    #end if
            
    #if $rdata_out

            </when>
            <when value="no" />
        </conditional>

        <conditional name="set_cosmic">
            <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param name="signum" type="integer" value="3" min="2" max="30"

                       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>
                </param>
            </when>
             <when value="no" />
        </conditional>
        <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
    </inputs>

        </data>
        <data name="cosmic" format="pdf" label="Cosmic signatures">
            <filter>set_cosmic['choices'] == "yes"</filter>
        </data>
        <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
            <filter>set_cosmic['choices'] == "yes" and set_cosmic['contrib_matrix_out'] == "yes"</filter>
        </data>

        <data name="rdata" format="rdata" label="${tool.name}: RData file">
            <filter>rdata_out</filter>
        </data>

    </outputs>
    <tests>
         <!-- cosmic signatures with cosmic V3 -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>
                    <element name="7" value="G.vcf"/>
                    <element name="8" value="H.vcf"/>
                    <element name="9" value="I.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
            <conditional name="set_spectrum">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="yes"/>
                <param name="contrib_matrix_out"  value="yes" />
                <param name="cosmic_version" value="v3"/>
            </conditional>
            <param name="signum" value="3" />
            <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
        </test>

         <!-- cosmic signatures -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>
                    <element name="7" value="G.vcf"/>
                    <element name="8" value="H.vcf"/>
                    <element name="9" value="I.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
            <conditional name="set_spectrum">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="yes"/>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="3" />
            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
        </test>

        <!-- cosmic signature on single sample -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" value="G.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <conditional name="set_spectrum">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="yes"/>
            </conditional>
            <param name="signum" value="5" />
            <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
        </test>

        <!-- simple profile -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" ftype="vcf" value="G.vcf"/>

            <param name="rdata_out" value="true" />
            <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
            <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
        </test>
    </tests>
    <help>

**What it does**