<tool id="pancancer_map_mutation_class" name="PAPAA: PanCancer map mutation class" version="@VERSION@">
  <description>map mutation class</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command><![CDATA['papaa_map_mutation_class.py' --version]]></version_command>
  <command><![CDATA[
      mkdir 'classifier' &&
      ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && 
      papaa_map_mutation_class.py
      --classifier_decisions 'classifier'
      #if $path_genes and str($path_genes):
      --path_genes '$path_genes'
      #end if
      @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
      @INPUT_FILENAME_RAW_MUT@
      > '${log}'
    ]]> 
  </command>
  <inputs>
    <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
    <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
    <expand macro="inputs_copy_number_file_conditional" />
    <expand macro="input_filename_raw_mut" />
  </inputs>
  <outputs>
    <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
    <data format="tabular" name="mutation_classification_scores" label="${tool.name} on ${on_string} (mutation_classification_scores.tsv)" from_work_dir="classifier/tables/mutation_classification_scores.tsv"/>
  </outputs>
  <tests>
        <test>
          <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
          <param name="path_genes" value="path_genes.txt" ftype="txt"/>
          <param name="copy_number" value="yes"/>
          <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/>
          <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/>
          <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/>
          <output name="log" file="map_mutation_class_Log.txt"/>
          <output name="mutation_classification_scores" file="mutation_classification_scores.tsv" />
        </test>
  </tests>
  <help><![CDATA[

    **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_map_mutation_class.py:**
      
      **Inputs:**
        --classifer_decisions   String of the location of folder containing classifier_decisions.tsv
        --path_genes  comma separated string of HUGO symbols for all genes in the pathway or Pathway genes list file
        --filename_copy_loss  Filename of copy number loss
        --filename_copy_gain  Filename of copy number gain
        --filename_raw_mut  Filename of raw mut MAF
        
      **Outputs:**
      Merge per sample classifier scores with mutation types present in each sample and generate "mutation_classification_scores.tsv" file  ]]>
    </help>
    <expand macro="citations" />
</tool>