<tool id="SAINT_ProteinInteractions_v2" name="SAINT Output to Protein Interaction File">
  <description></description>
  <command interpreter="python">ProteinInteractions_v2.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>
**Protein Interactions**

This program will read in a SAINT 'list.txt' file and the interactions from ConsensusPathDB ( http://consensuspathdb.org/ ) and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting protein-protein interactions (PPI's) so that it doesn't affect our SAINT score or include interactions that don't score well.

INPUT

SAINT Output: SAINTexpress output.

SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1).

Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1).
 * low: no filtering
 * medium: >0.5
 * high: >0.7
 * very high: >0.9

Species: Human, Yeast, or Mouse.

  </help>
</tool>