view oncoprintplus.xml @ 4:2877b1ba1250 draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="oncoprintplus" name="OncoPrintPlus" version="1.0.0">

  <description>
    creates a summary matrix plot of cohort wide mutations
  </description>

  <macros>
      <import>citations.xml</import>
  </macros>

  <requirements>
    <requirement type="binary">Rscript</requirement>    
    <requirement type="package" version="3.2.1">R</requirement>
    <requirement type="package" version="1.0">cancer_genomics_functions</requirement>
    <requirement type="environment" verion="1.0">CANCER_GENOMICS_FUNCTIONS_PATH</requirement>
    <requirement type="package" version="5.3.4">boutroslab_plotting_general</requirement>
  </requirements>

  <command detect_errors="aggressive">

    touch output.pdf;
    Rscript $__tool_directory__/oncoprintplus.R
      --input_snv $input_maf
      --cancer_genomics_functions_path \$CANCER_GENOMICS_FUNCTIONS_PATH/

      #if $gene.order.value == "default"

      #else
        --gene_order $gene.order
      #end if
      
      #if $gene.gene_list
        --gene_list $gene.gene_list
      #end if
      
      #if $gene.snv_counts
        --plot_gene_snv_counts
      #end if
      
      #if $gene.mutsig.plot
        --plot_gene_mutsig
      #end if

      #if $gene.mutsig.mutsig
        --gene_mutsig $gene.mutsig.mutsig
      #end if
      
      #if $gene.oncodrive.plot
        --plot_gene_oncodrive
      #end if

      #if $gene.oncodrive.oncodrive
        --gene_oncodrive $gene.oncodrive.oncodrive
      #end if

      #if $patient.covariates.use_covariates == "no":

        #if $patient.covariates.order.value == "default":

        #else
          --patient_order snv_counts 
        #end if

      #else
        
        --patient_covariate_data $patient.covariates.covariate_data

        #for $item in $patient.covariates.plot:
          --plot_patient_covariate $item.covariate_to_plot
        #end for

        #for $item in $patient.covariates.order:
            --patient_order $item.covariate_or_internal.order
        #end for

      #end if

      #if $patient.snv_counts
        --plot_patient_snv_counts
      #end if

      #if $patient.snv_distribution
        --plot_patient_snv_distribution
      #end if

      --center_plot $center_plot
      --output ./output.pdf;

      mv output.pdf $output;

  </command>

  <inputs>
    
    <param type="data" format="maf" name="input_maf" label="Cohort Wide MAF File"/>
    
    <param type="select" name="center_plot" label="Central Plot">
      <option value="impact" selected="True">VCF2MAF IMPACT</option>
      <option value="variant_classification">Variant Classification</option>
    </param>

    <section name="gene" title="Gene Related Inputs" expanded="False">
      <param type="select" name="order" label="Order of Genes">
        <option value="default" selected="True">Order in MAF</option>
        <option value="snv_counts">SNV Counts</option>
        <option value="mutsig">MutSigCV Data</option>
        <option value="oncodrive">Oncodrive-FM Data</option>
      </param>
      <param type="boolean" name="snv_counts" label="Plot Gene SNV Counts" checked="true"/>
      <param type="data" format="txt" name="gene_list" label="List of Genes Include" optional="true"/>
      <section name="mutsig" title="MutsigCV Inputs" expanded="False">
        <param type="boolean" name="plot" label="Plot MutSigCV Data" checked="false"/>
        <param type="data" format="txt" name="mutsig" label="Mutsig Input" optional="true"/>
      </section>
      <section name="oncodrive" title="Oncodrive-FM Inputs" expanded="False">
        <param type="boolean" name="plot" label="Plot Oncodrive-FM Data" checked="false"/>
        <param type="data" format="txt" name="oncodrive" label="Oncodrive-FM Input" optional="true"/>
      </section>
    </section>
    <section name="patient" title="Patient Related Inputs" expanded="False">
      <conditional name="covariates">
        <param name="use_covariates" type="select" label="Use Patient Covariates">
          <option value="no" selected="True">No</option>
          <option value="yes">Yes</option>
        </param>
        <when value="no">
          <repeat name="order" title="Patient Order" default="1">
            <param type="select" name="order" label="Order of Patients">
              <option value="default" selected="True">Order in MAF</option>
              <option value="snv_counts">SNV Counts</option>
            </param>
          </repeat>
        </when>
        <when value="yes">
          <param type="data" format="tabular" name="covariate_data" label="Patient Covariate File"/>
          <repeat name="plot" title="Plot Patient Covariate" default="1">
            <param type="text" name="covariate_to_plot" label="Plot Patient Covariate" />
          </repeat>
          <repeat name="order" title="Patient Order" default="1">
            <conditional name="covariate_or_internal">
             <param name="use_covariate_or_internal" type="select" label="Order on">
              <option value="cov" selected="True">Covariate</option>
              <option value="int">Other</option>
            </param>
            <when value="cov">
              <param type="select" name="order" label="Order of Patients">
                <option value="default" selected="True">Order in MAF</option>
                <option value="snv_counts">SNV Counts</option>
              </param>              
            </when>
            <when value="int">
              <param name="order" type="text" title="Order of Patients"/>
            </when>
            </conditional>
          </repeat>
        </when>
      </conditional>
      <param type="boolean" name="snv_counts" label="Plot Patient SNV Counts" checked="true"/>
      <param type="boolean" name="snv_distribution" label="Plot Patient SNV Distribution" checked="true"/> 
    </section>
  </inputs>
  <outputs>
    <data format="pdf" name="output"/>
  </outputs>
  <help>
  https://labs.oicr.on.ca/boutros-lab/software/bpg
  </help>
  <citations>
      <expand macro="morinlab_citation"/>
      <expand macro="galaxy_citation"/>
  </citations>  
</tool>