comparison mutational_patterns.xml @ 24:ca6c19ee7da0 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d

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>
        <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>
<!--
install more bioconda genomes
bioconductor-bsgenome.mmusculus.ucsc.mm9
bioconductor-bsgenome.mmusculus.ucsc.mm10
-->

            <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"/>
                    <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_preset">
                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="user_signatures" />
                    <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
                </conditional>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="4" />
            <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
        </test>
         <!-- cosmic v3.2 -->
        <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_preset">
                <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"/>
        </test>
         <!-- cosmic v2 -->
        <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_preset">
                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="cosmic" />
                    <param name="cosmic_version" value="v2"/>
                </conditional>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="3" />
            <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
        </test>
        <!-- simple spectrum -->
        <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_preset">
                <param name="choices" value="no"/>
            </conditional>
            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
        </test>
         <!-- de novo signatures -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>

            <param name="newsignum" value="4" />
            <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**

24:ca6c19ee7da0

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0">
    <description>from genomic variations in vcf files</description>
    <requirements>
        <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
        <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> -->
        <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
        <requirement type="package" version="1.7.1=r41hc72bb7e_0">r-optparse</requirement>
        <requirement type="package" version="0.2.21=r41h7525677_1">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_4">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
        <requirement type="package" version="1.4.4=r41hdfd78af_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
<!--
install more bioconda genomes
bioconductor-bsgenome.mmusculus.ucsc.mm9
bioconductor-bsgenome.mmusculus.ucsc.mm10
-->

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

    </outputs>
    <tests>
         <!-- de novo signatures -->
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="6" value="F.vcf"/>

            <param name="newsignum" value="4" />
            <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>
         <!-- 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"/>
                    <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_preset">
                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="user_signatures" />
                    <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
                </conditional>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="4" />
            <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
        </test>
         <!-- cosmic v3.2 -->
        <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_preset">
                <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"/>
        </test>
         <!-- cosmic v2 -->
        <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_preset">
                <param name="choices" value="yes"/>
                <conditional name="set_signature_input">
                    <param name="input_signature_choices" value="cosmic" />
                    <param name="cosmic_version" value="v2"/>
                </conditional>
                <param name="contrib_matrix_out"  value="yes" />
            </conditional>
            <param name="signum" value="3" />
            <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
            <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
        </test>
        <!-- simple spectrum -->
        <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_preset">
                <param name="choices" value="no"/>
            </conditional>
            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help>

**What it does**