# HG changeset patch
# User rsajulga
# Date 1526610771 14400
# Node ID 7f319af8c5b39bf032ed54f1e74e1ccdbf71e9b8
# Parent  676c8be98be45d1c51ba8c8b99ed87a265b96761
Uploaded

diff -r 676c8be98be4 -r 7f319af8c5b3 cravat_submit.xml
--- a/cravat_submit.xml	Thu May 17 22:32:25 2018 -0400
+++ b/cravat_submit.xml	Thu May 17 22:32:51 2018 -0400
@@ -1,6 +1,6 @@
 <tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
     <description>Submits, checks for, and retrieves data for cancer annotation</description>
-  <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $output1 $output2 $output3 $output4</command>
+  <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $Variant $Gene $Noncoding $Error</command>
   
   
   <inputs>
@@ -16,16 +16,18 @@
       <option value="GRCh38">GRCh38/hg38</option>
       <option value="GRCh37">GRCh37/hg19</option>
     </param>
-    <param format="tabular" name="psm" type="data" optional="true" label="Peptide Spectrum Match Report (Optional)"> </param>
+    <param format="tabular" name="psm" type="data" optional="true" label="ProBED File(Optional)"> </param>
     
     
   </inputs>
   
   <outputs>
-    <data format="cravat" label="CRAVAT: Variant Report" name="output1" />
-    <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="output2" />
-    <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="output3" />
-    <data format="cravat" label="CRAVAT: Errors" name="output4" />
+      <collection name="collection" type="list" label="CRAVAT: ${on_string} using ${dropdown}">
+        <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="Gene" />
+        <data format="cravat" label="CRAVAT: Variant Report" name="Variant" />
+        <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="Noncoding" />
+        <data format="cravat" label="CRAVAT: Errors" name="Error" />
+      </collection>
   </outputs>
 
   <tests>