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changeset 4:d5580071d910

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Update commandline to detect successful completion
author Jim Johnson <jj@umn.edu>
date Mon, 11 Nov 2013 11:08:56 -0600
parents a9d882069cd4
children a67c0a0d24ac
files trinityrnaseq.xml
diffstat 1 files changed, 7 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/trinityrnaseq.xml	Fri Nov 08 16:11:37 2013 -0600
+++ b/trinityrnaseq.xml	Mon Nov 11 11:08:56 2013 -0600
@@ -40,11 +40,13 @@
 				--bfly_opts " $additional_params.bfly_opts "
 			#end if
         #end if
-	
-                
-        ## direct to output
-        | tee $trinity_log | grep -q 'All commands completed successfully.'
- 
+
+        ## direct output to the log file
+        | tee $trinity_log 
+        ## Check output for success message (direct grep output to dev null, -q option quits early leaving tee error messages)
+        | grep 'All commands completed successfully.' > /dev/null
+        ## Print the stats to output to provide info on galaxy history item
+        &amp;&amp; \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
     </command>
     <inputs>
         <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
@@ -115,10 +117,6 @@
                source="both" 
                level="fatal" 
                description="Trinity.pl not found" />
-        <regex match="Error" 
-               source="both" 
-               level="fatal" 
-               description="A trinity process failed" />
     </stdio>
     <outputs>
         <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />