# HG changeset patch
# User bornea
# Date 1454016690 18000
# Node ID 8f6b0b0b242c8c4c3712c17140d8a99c941fc32d
# Parent  bb16012603662a09121567158d46cf0ea76fe61a
Uploaded

diff -r bb1601260366 -r 8f6b0b0b242c saint_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saint_wrapper.xml	Thu Jan 28 16:31:30 2016 -0500
@@ -0,0 +1,38 @@
+<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 \$INSTALL_RUN_PATH/</command>
+  <requirements>
+    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
+  </requirements>
+  <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>
+    <!--
+      AB: Needs some help probably copy paste from Saint manual if that is okay.
+    -->
+  </help>
+</tool>