<tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_2">
    <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="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
        <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
        <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
        <!-- install bioconda genomes
        bioconductor-bsgenome.mmusculus.ucsc.mm9
        bioconductor-bsgenome.mmusculus.ucsc.mm10   -->                    
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>

    <command detect_errors="exit_code"><![CDATA[ 
#import json
#import os
Rscript $__tool_directory__/mutational_patterns.R 
    --inputs
    #set $filename_to_element_identifiers = {}
    #for $sample in $vcfs:
        $filename_to_element_identifiers.__setitem__(str($sample),  $sample.element_identifier)
    #end for
    '#echo json.dumps(filename_to_element_identifiers)#'
    --genome '$genome'
    --levels '$levels'
    --signum '$signum'
    --output '$output'
            
]]></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="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option>
            <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
            <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
            <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
            <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
        </param>
        <param name="levels" type="data" format="tabular"
               label="A two-column tab-separated file describing levels attributed to each sample name"
               help="Tip: the sample name list in the vcf collection can be obtained using
               the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
               example:&lt;br&gt;
               sample1 female&lt;br&gt;
               sample2 female&lt;br&gt;
               sample3 male&lt;br&gt;
               sample4 female&lt;br&gt;
               sample5 male&lt;br&gt;
               sample5 male" />
        <param name="signum" type="integer" value="2" 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"/>

    </inputs>
    <outputs>
        <data name="output" format="pdf" label="Mutational Patterns/Signatures" />
    </outputs>
    <tests>
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="1" value="EGF167.vcf"/>
                    <element name="2" value="EGF089.vcf"/>
                    <element name="3" value="EGF037F.vcf"/>
                </collection>
            </param>
            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
            <param name="levels" value="levels.tab" ftype="tabular"/>
            <param name="signum" value="3" />
            <output name="output" file="output.pdf" compare="sim_size" ftype="pdf"/>
        </test>
    </tests>
    <help>

**What it does**

Takes as inputs

* a collection of n vcf files corresponding to n samples.
* a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
* the number of cosmic signatures to decompose mutational patterns of samples


This tool returns a pdf file with the visualisation :

* the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
* the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
* the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns  (to be set by the user, between 2 and 30)
* a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
* pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern

.. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt

    </help>
    <citations>
        <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
        <citation type="doi">10.1186/s13073-018-0539-0</citation>
        <citation type="doi">10.1038/nature12477</citation>
    </citations>
</tool>