# HG changeset patch
# User bornea
# Date 1447173617 18000
# Node ID eb820d9b69dda19da7de7ab933e8c03b8dd656e6
# Parent  d963be0ebf537a03e241f0745b893e925a15c84c
Uploaded

diff -r d963be0ebf53 -r eb820d9b69dd saint_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saint_wrapper.xml	Tue Nov 10 11:40:17 2015 -0500
@@ -0,0 +1,32 @@
+<tool id="saint_wrapper" name="SAINT">
+  <description></description>
+  <command interpreter="python">saint_wrapper.py $inter_input $prey_input $bait_input $rep_num $vc_bool $vc_num $go_bool $go_file $output</command>
+  <inputs>
+    <param format="txt" name="inter_input" type="data" label="Interactions File"/>
+    <param format="txt" name="prey_input" type="data" label="Prey File"/>
+    <param format="txt" name="bait_input" type="data" label="Bait File"/>
+    <param name="rep_num" type="integer" value="100" label="Number of Replicates" help="the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait.  This option is useful when some baits have more replicates than others." />
+    <param type="boolean" name="vc_bool" checked="false" label="Using Virtual Control Purifications by Compression"/>
+    <param name="vc_num" type="integer" value="1" label="Number of Virtual Controls" />
+    <param type="boolean" name="go_bool" checked="false" label="Incorporate External Data Sources" />
+    <param format="txt" name="go_file" type="data" optional="true" label="External Data File" help="SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability."/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </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>
+  </help>
+</tool>