view oncostrip.xml @ 5:b78c81a7ebaf draft

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<tool id="oncostrip" name="Oncostrip Plot" version="0.9.30">

  <description>
    Cohort-wide mutation oncostrip from MAF and (optionally) GISTIC data
  </description>

  <command detect_errors="aggressive">

      mkdir outputs;
      touch gene_list.txt;
      #if $gene_input_type.gene_input_type_selector.value == "other":
        echo $gene_input_type.gene > gene_list.txt;
      #else:
        cat $gene_input_type.gene_file > gene_list.txt;
      #end if

      Rscript $__tool_directory__/oncostrip_gistic.R
        --input_maf $input_maf
        --gene_list gene_list.txt
        --output_plot $output_plot
      #if $include_anno.anno == "use_anno":
        --anno $include_anno.anno_file
      #end if
      #if $sort_by == "anno":
        --sort_by anno
      #elif $sort_by == "gene":
        --sort_by gene
      #else:
        --sort_by $sort_by 
      #end if
      #if $include_gistic.gistic == "use_gistic":
      -gal $include_gistic.file1
      -ga $include_gistic.file2
      -gd $include_gistic.file3
      #end if
      ;
      
  </command>

  <inputs>
    <param type="data" format="maf" name="input_maf" label="MAF File"/>
    <conditional name="gene_input_type">
      <param name="gene_input_type_selector" type="select" label="Choose how to input genes">
        <option value="file" selected="True">Gene File</option>
        <option value="other">Other</option>
      </param>
      <when value="file">
        <param name="gene_file" type="data" format="txt" label="Gene File"  help="list of genes separated by newlines" />
      </when>
      <when value="other">
        <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
      </when>
    </conditional>

    <param name="sort_by" type="select" label="Sort samples and genes in output?">
      <option value="none">No sorting</option>
      <option value="gene">Sort genes and patients using mutation frequency</option>
      <option value="anno">Sort on annotation, then mutation frequency</option>
    </param>

    <conditional name="include_anno">
    <param name="anno" type="select" display="radio" label="Optional: include annotation information for each sample">
	<option value="use_anno" checked="false">Include</option>
        <option value="no_anno" checked="true">Do not include</option>
    </param>
    <when value="use_anno">
      <param name="anno_file" type="data" format="txt" optional="true" label="Annotation file"  help="text file with the first column listing each sample and remaining columns reserved for annotation" />

      
    </when>
    </conditional>
    <conditional name="include_gistic">
      <param name="gistic" type="select" display="radio" label="Optional: include GISTIC output in display">
	<option value="use_gistic" checked="false">Include</option>
	<option value="no_gistic" checked="true">Do not include</option>
      </param>
      <when value="use_gistic">
	<param name="file1" type="data" format="txt" label="all_lesions"  help="all_lesions output from GISTIC" />
	<param name="file2" type="data" format="txt" label="amp_genes"  help="amp_genes output from GISTIC" />
	<param name="file3" type="data" format="txt" label="del_genes"  help="del_genes output from GISTIC" />
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data format="pdf" name="output_plot"/>
  </outputs>
  <citations>
    <citation type="bibtex">
      @article {Albuquerque089631,
      author = {Albuquerque, Marco A and Grande, Bruno M and Ritch, Elie and Jessa, Selin and Krzywinski, Martin I and Grewal, Jasleen and Shah, Sohrab and Boutros, Paul and Morin, Ryan},
      title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
      year = {2016},
      doi = {10.1101/089631},
      publisher = {Cold Spring Harbor Labs Journals},
      URL = {http://biorxiv.org/content/early/2016/11/26/089631},
      eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
      journal = {bioRxiv}
      }

    </citation>
    <citation type="bibtex">
      @misc{
      goecks2010galaxy,
      title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
      author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
      journal={Genome Biol},
      volume={11},
      number={8},
      pages={R86},
      year={2010}
      }
    </citation>
    <citation type="doi">10.1101/052662</citation>
    </citations>
</tool>