comparison mutational_patterns.xml @ 3:e332cf9dfa06 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"

2:aea952be68cb

<tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0+galaxy3">
    <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>

    #if $set_denovo.choices == 'yes':
        --nrun $set_denovo.nrun
        --rank $set_denovo.rank
        --newsignum $set_denovo.newsignum
        --output_denovo $denovo
    #end if

    #if $set_cosmic.choices == 'yes':
        --signum '$set_cosmic.signum'
        --output_cosmic $cosmic
    #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">
            <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>

                <option value="no">No</option>
            </param>
            <when value="yes" />
            <when value="no" />
        </conditional>
        <conditional name="set_denovo">
            <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>

                <param name="nrun" type="integer" value="10" min="10" max="200"
                       label="Number of cycles to find best fitting of signatures"
                       help="High values extend the computational time"/>
                <param name="rank" type="integer" value="4" min="3" max="30"
                       label="Number of ranks to be displayed for control of optimal number of signature"
                       help="High values extend the computational time"/>
                <param name="newsignum" type="integer" value="4" min="2" max="30"
                       label="Number of de novo signatures to capture"
                       help="High values extend the computational time"/>
            </when>
            <when value="no" />
        </conditional>

        <conditional name="set_cosmic">

            </param>
            <when value="yes">
                <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 30 signature types from cosmic"/>
            </when>
             <when value="no" />
       </conditional>
    </inputs>
    <outputs>
        <data name="spectrum" format="pdf" label="Mutational Spectrum">
            <filter>set_spectrum['choices'] == "yes"</filter>
        </data>
        <data name="denovo" format="pdf" label="De novo signatures">
            <filter>set_denovo['choices'] == "yes"</filter>
        </data>
        <data name="cosmic" format="pdf" label="Cosmic signatures">
            <filter>set_cosmic['choices'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" ftype="vcf" value="G.vcf"/>
                    <element name="2" ftype="vcf" value="H.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <param name="levels" value="GH_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"/>
            </conditional>
            <param name="signum" value="3" />
            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
        </test>
        <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>
            <conditional name="set_cosmic">
                <param name="choices" value="no"/>
            </conditional>
            <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
        </test>
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" ftype="vcf" value="G.vcf"/>
                    <element name="2" ftype="vcf" value="H.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <conditional name="set_levels">
                <param name="choices" value="yes"/>
            </conditional>
            <param name="levels" value="GH_levels.tab" ftype="tabular"/>
            <conditional name="set_spectrum">
                <param name="choices" value="yes"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="no"/>
            </conditional>
            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
        </test>
    </tests>
    <help>

**What it does**

3:e332cf9dfa06

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy4">
    <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>

    #if $set_denovo.choices == 'yes':
        --nrun $set_denovo.nrun
        --rank $set_denovo.rank
        --newsignum $set_denovo.newsignum
        --output_denovo $denovo
        --sigmatrix $sigmatrix
    #end if

    #if $set_cosmic.choices == 'yes':
        --cosmic_version $set_cosmic.cosmic_version
        --signum '$set_cosmic.signum'
        --output_cosmic $cosmic
    #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">
            <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>

                <option value="no">No</option>
            </param>
            <when value="yes" />
            <when value="no" />
        </conditional>

        <conditional name="set_denovo">
            <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>

                <param name="nrun" type="integer" value="10" min="10" max="200"
                       label="Number of cycles to find best fitting of signatures"
                       help="High values extend the computational time"/>
                <param name="rank" type="integer" value="4" min="3" max="30"
                       label="Number of ranks to be displayed for control of optimal number of signature"
                       help="High values extend the computational time. In addition the number of ranks cannot be greater than the number of available samples in the study"/>
                <param name="newsignum" type="integer" value="4" min="2" max="30"
                       label="Number of de novo signatures to capture"
                       help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
            </when>
            <when value="no" />
        </conditional>

        <conditional name="set_cosmic">

            </param>
            <when value="yes">
                <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 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>
            </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>
    <outputs>
        <data name="spectrum" format="pdf" label="Mutational Spectrum">
            <filter>set_spectrum['choices'] == "yes"</filter>
        </data>
        <data name="denovo" format="pdf" label="De novo signatures">
            <filter>set_denovo['choices'] == "yes"</filter>
        </data>
        <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix">
            <filter>set_denovo['choices'] == "yes"</filter>
        </data>
        <data name="cosmic" format="pdf" label="Cosmic signatures">
            <filter>set_cosmic['choices'] == "yes"</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"/>
                    <element name="2" ftype="vcf" value="H.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <conditional name="set_levels">
                <param name="choices" value="yes"/>
            </conditional>
            <param name="levels" value="GH_levels.tab" ftype="tabular"/>
            <conditional name="set_spectrum">
                <param name="choices" value="yes"/>
            </conditional>
            <conditional name="set_denovo">
                <param name="choices" value="no"/>
            </conditional>
            <conditional name="set_cosmic">
                <param name="choices" value="no"/>
            </conditional>
            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
        </test>

         <!-- de novo signatures -->
        <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>
            <conditional name="set_cosmic">
                <param name="choices" value="no"/>
            </conditional>
            <param name="nrun" value="10" />
            <param name="rank" value="4" />
            <param name="newsignum" value="4" />
            <param name="rdata_out" value="true" />
            <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
            <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" 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="GH_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"/>
            </conditional>
            <param name="signum" value="3" />
            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
        </test>
    </tests>
    <help>

**What it does**