<tool id="SAINT_ProteinInteractions" name="SAINT Output to Protein Interaction File">
  <description></description>
  <command interpreter="python">ProteinInteractions.py $input $saint_cutoff $CPDB_cutoff $species $Cytoscape_File \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="input" type="data" label="SAINT Output"/>
    <param type="float" name="saint_cutoff" label="Saint Score Cutoff" value="0.8"/>
    <param type="float" name="CPDB_cutoff" label="Consensus Path Database Score Cutoff" value="0.8"/>
    <param type="select" name="species" label="Species">
      <option value="Human">Human</option>
      <option value="Yeast">Yeast</option>
      <option value="Mouse">Mouse</option>
    </param>
  </inputs>
  <outputs>
    <data format="sif" name="Cytoscape_File" label="Cytoscape File"/>    
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
  </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>
SAINT Output to Protein Interaction File
----------------------------------------

This tool reads in a *list.txt* file from SAINTexpress and the
interactions from ConsensusPathDB (http://consensuspathdb.org/) and
returns all the known protein-protein interactions observed in the
experiment as a simple interaction file (.SIF).

    **Note:** This network will not include identified interactions
    between baits and preys. This tool queries known interactions
    between preys only

**1) SAINT Output File**

SAINTexpress generated *list.txt* file.

    **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
    "EGFR\_HUMAN" or "P00533").

**2) SAINT Score Cutoff**

SaintScore filter in range 0-1 (default 0.8)

**3) Consensus Path Database Score Cutoff**

Interaction confidence filter in range 0-1 (default 0.8) to specify
which protein interactions in ConsensusPathDB to include.

**4) Species**

Please specify species. Supported species are Human, Mouse, and Yeast.
  </help>
</tool>