# HG changeset patch
# User bornea
# Date 1462978263 14400
# Node ID e3625c710dd3b3aec2f7955b8e4785eaac67f504
# Parent  46a582eb1ea9f9b3b72227b366da6295e8316d0e
Uploaded

diff -r 46a582eb1ea9 -r e3625c710dd3 nsaf_scoring.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nsaf_scoring.xml	Wed May 11 10:51:03 2016 -0400
@@ -0,0 +1,38 @@
+<tool id="nsaf_scoring" name="NSAF Scoring Table">
+  <description></description>
+  <command interpreter="python">nsaf_scoring.py $list_file $prey_file $crapome $inter_file $outfile \$INSTALL_RUN_PATH/ </command>
+  <requirements>
+    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
+  </requirements>
+  <inputs>
+    <param format="txt" name="list_file" type="data" label="List File"/>
+    <param format="txt" name="prey_file" type="data" label="Prey File"/>
+    <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
+    <param format="txt" name="inter_file" type="data" label="Inter File" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="outfile" label="NSAF Scored Table"/>    
+  </outputs>
+  <stdio>
+    <regex match="ValueError: 'PreyGene' is not in list"
+       source="stdout"
+       level="fatal"
+       description="Error: Check Input file."/>
+    <regex match="Error|error"
+     source="stdout"
+           level="fatal"
+           description="Unknown error"/>
+    <regex match="Error|error"
+     source="stderr"
+           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>
\ No newline at end of file