# HG changeset patch
# User bornea
# Date 1447175733 18000
# Node ID 73476fc784ccaf8867a2c092eb933f92a2874ef5
# Parent  9f9e80281b6405b15a9d1a70b26522dc98c0874c
Uploaded

diff -r 9f9e80281b64 -r 73476fc784cc saint_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saint_wrapper.xml	Tue Nov 10 12:15:33 2015 -0500
@@ -0,0 +1,35 @@
+<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>
+  <requirements>
+    <requirement type="package">saintexpress</requirement>
+  </requirements>
+  <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>