--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInteractions_v2.xml	Fri Jan 29 12:52:19 2016 -0500
@@ -0,0 +1,53 @@
+<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"
+	   source="stdout"
+           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>
+**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
+
+4) Species: Human, Yeast, or Mouse.
+
+  </help>
+</tool>
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