# HG changeset patch
# User bornea
# Date 1461958957 14400
# Node ID edde2724910f2981d779830842f1360894112854
# Parent  378fc3676c788ba5872a7cc834adb6776e165126
Uploaded

diff -r 378fc3676c78 -r edde2724910f CRAPomeQuery.xml
--- a/CRAPomeQuery.xml	Fri Apr 29 15:42:22 2016 -0400
+++ b/CRAPomeQuery.xml	Fri Apr 29 15:42:37 2016 -0400
@@ -1,6 +1,6 @@
 <tool id="CRAPomeQuery" name="Query CRAPome">
   <description></description>
-  <command interpreter="python">CRAPomeQuery.py $input $species $CrapomeFile \$INSTALL_RUN_PATH/</command>
+  <command interpreter="python">CRAPomeQuery.py $input $species $fasta_db $CrapomeFile \$INSTALL_RUN_PATH/</command>
   <requirements>
     <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
   </requirements>
@@ -10,6 +10,7 @@
       <option value="HUMAN">Human</option>
       <option value="YEAST">Yeast</option>
     </param>
+    <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" optional="true"/>
   </inputs>
   <outputs>
     <data format="txt" name="CrapomeFile" label="CRAPome File"/>    
@@ -46,5 +47,9 @@
 **2) Species**
 
 Please specify species. Supported species are Human and Yeast.
+
+**3) Uniprot Fasta Database**
+
+A uniprot database can be provided that will be used to get gene names.  
   </help>
 </tool>
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