<tool id="Protein_report_processig" name="SAINT pre-processing Peptideshaker Report">
  <description></description>
  <command interpreter="python">Protein_report_processing.py $input $Bait_file $use_metric $fasta_db $preybool 
    "
      #for $ba in $bait
       ${ba.bait1}
       ${ba.assign}
       ${ba.T_C}
      #end for
    "
    \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" muliple="true"/>
    <param type="use_metric" name="type" label="Select Report File Value for Qunatification">
      <option value="#Validated Peptides">#Validated Peptides</option>
      <option value="#Peptides">#Peptides</option>
      <option value="#Unique">#Unique</option> 
      <option value="#Validated PSMs">#Validated PSMs</option>
      <option value="#PSMs">#PSMs</option> 
    </param>
    <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
    <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" optional="true"/>
    <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
    <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
    <repeat name="bait" title="Bait Create">
      <param name="bait1" type="text" size="100" label="Bait"/>
      <param name="assign" type="text" size="100" label="Group Assignment"/>
      <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
    </repeat>

  </inputs>
  <outputs>
    <data format="txt" name="Inter_file" label="Inter File"/>    
    <data format="txt" name="Prey_file" label="Prey File" />
    <data format="txt" name="Bait_file" label="Bait File" />
  </outputs>
  <stdio>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
    <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
           source="stderr"
           level="fatal"
           description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
    <regex match="bait_temp_file = open(sys.argv[10], 'r')"
           source="stderr"
           level="fatal"
           description="Error: Bait create settings mismatch. Check job settings."/>
    <regex match="Error|error"
	   source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
  </stdio> 

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
  </help>
</tool>