<?xml version="1.0"?>
<tool id="selectproteinids" name="Filter ids" version="1.0" hidden="false">
  
  <description></description>
  <command interpreter="perl">
    selectproteinids.pl $input $maintaincon $out_file
  </command>

  <inputs>
    <param format="tabular" name="input" type="data" label="Input table"/>

    <param name="maintaincon" type="select" display="radio" label="Maintain contaminants">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>

  </inputs>

  <outputs>
    <data format="tabular" name="out_file" label="${input.name} filtered"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="protein_ids_simple.csv"/>
      <param name="maintaincon" value="yes"/>
      <output name="out_file" file="proteinGroups_csv_filtered_with_contaminants.tabular"/>
    </test>

    <test>
      <param name="input" value="protein_ids_simple.csv"/>
      <param name="maintaincon" value="no"/>
      <output name="out_file" file="proteinGroups_csv_filtered_without_contaminants.tabular"/>
    </test>

  </tests>

  <help>

    Input: Protein Groups from MaxQuant


    Output: Table with id's got from MaxQuant Protein Groups

  </help>

  <citations>
    <citation type="bibtex">
      @misc{Concatenate,
        author = {Application, Labis},
        year = 2018,
        title = Concatenate,
        publisher = labisapplications
      }
    </citation>
  </citations>
</tool>