<tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
  
<requirements>
  <requirement type="package" version="1.4.0">bioconductor-fgsea</requirement>
  <requirement type="package" version="1.20.0">r-getopt</requirement>
  <!-- required for alpha function used with plotMD -->
  <requirement type="package" version="0.12.13">r-rcpp</requirement>
</requirements>

<command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/GSEA.R' --input1 '$Ranked_list' --input2 '$Pathway_database' --output '$output'
    ]]></command>
  <inputs>
    <param type="data" name="Ranked_list" format="txt" />
    <param type="data" name="Pathway_database" format="txt" />
  </inputs>
  <outputs>
    <data name="output" format="txt" />
  </outputs>
  <tests>
    <test>
      <param name="Ranked_list" value="ranked_genes_list.rnk"/>
      <param name="Pathway_database" value="ouse.gmt"/>
      <output name="output" file="GSEA_results.txt"/>
    </test>
  </tests>
  <help><![CDATA[
        Write the tool help section here.
    ]]></help>
  <citations>
    <citation type="bibtex">
      @misc{github01_mismatch_removal,
      author = {LastTODO, FirstTODO},
      year = {TODO},
      title = {01_mismatch_removal},
      publisher = {GitHub},
      journal = {GitHub repository},
      url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
      }</citation>
  </citations>
</tool>