comparison mutational_patterns.xml @ 14:56c8869a231e draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"

13:6741b819cc15

<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy13.1">
    <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.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 = {}

]]></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>

* 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>

14:56c8869a231e

<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>
-->
<!--
install more 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 = {}

]]></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>

* 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 to their mutational pattern

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

    </help>
    <citations>