diff star_fusion.xml @ 4:c53938d8a6da draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 38b164ccb9b3cdfb58d83cdc1f05063a40123bab-dirty

--- a/star_fusion.xml	Wed Aug 24 07:18:07 2016 -0400
+++ b/star_fusion.xml	Fri Aug 26 04:45:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-1" profile="16.07">
+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
     <description>detect fusion genes in RNA-Seq data</description>
     <requirements>
         <!-- Bio-conda -->
@@ -6,6 +6,10 @@
     </requirements>
 
     <stdio>
+        <regex match="command not found" source="stderr" level="fatal"/>
+        <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
+        <regex match="FATAL ERROR" source="stderr" level="fatal"/>
+        
         <regex match="Warning:" source="stderr" level="warning"/>
         <regex match="CMD:" source="stderr" level="warning"/>
         
@@ -106,7 +110,10 @@
             <when value="cached">
                 <param name="ownFile"
                        type="select" label="Genome to search">
-                    <options from_data_table="all_fasta" />
+                    <options from_data_table="all_fasta">
+                        <column name="value" index="3"/>
+                        <column name="dbkey" index="1"/>
+                    </options>
                 </param>
             </when>
             <when value="history">