comparison mutational_patterns.xml @ 25:b00fef2b1c2c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd

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>

        --nrun '$set_denovo.nrun'
        --rank '$set_denovo.rank'
        --newsignum '$set_denovo.newsignum'
        --output_denovo '$denovo'
        --sigmatrix '$sigmatrix'
    #end if

    #if $set_preset.choices == 'yes':

        #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'

                       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_preset">

                <param name="choices" value="yes"/>
            </conditional>
            <conditional name="set_preset">
                <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"/>
            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
            <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
        </test>

**Inputs**

* a collection of VCF files with somatic mutations calls from analysis of samples.
* a tabular table describing the correspondance of sample names to levels of a factor
(tissues, ages, sexes, etc.)

**Outputs**

This tool returns pdf files with various visualisations of :

25:b00fef2b1c2c

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy1">
    <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>

        --nrun '$set_denovo.nrun'
        --rank '$set_denovo.rank'
        --newsignum '$set_denovo.newsignum'
        --output_denovo '$denovo'
        --sigmatrix '$sigmatrix'
        --cosmic_id_threshold '$set_denovo.cosmic_id_threshold'
    #end if

    #if $set_preset.choices == 'yes':

        #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'

                       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"/>
                <param name="cosmic_id_threshold" type="float" value="0.85" min="0" max="1"
                       label="Minimum cosine similarity to rename a signature"
                       help="If a signature has a cosine similarity higher than this value with a cosmic v3.2 signature, it will renamed accordingly, with a -like suffix"/>
            </when>
            <when value="no" />
        </conditional>

        <conditional name="set_preset">

                <param name="choices" value="yes"/>
            </conditional>
            <conditional name="set_preset">
                <param name="choices" value="no"/>
            </conditional>
            <param name="nrun" value="30" />
            <param name="rank" value="4" />
            <param name="newsignum" value="2" />
            <param name="cosmic_id_threshold" value="0.84" />
            <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>

**Inputs**

* a collection of VCF files with somatic mutations calls from analysis of samples.
* a tabular table describing the correspondance of sample names to levels of a factor
  (tissues, ages, sexes, etc.)

**Outputs**

This tool returns pdf files with various visualisations of :