Mercurial > repos > jjohnson > trinityrnaseq
diff trinityrnaseq.xml @ 4:d5580071d910
Update commandline to detect successful completion
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 11 Nov 2013 11:08:56 -0600 |
| parents | a9d882069cd4 |
| children | 09c1e388c20c |
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--- 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 $trinity_log + ## Check output for success message (direct grep output to dev null, -q option quits early leaving tee error messages) + | grep 'All commands completed successfully.' > /dev/null + ## Print the stats to output to provide info on galaxy history item + && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta </command> <inputs> <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction"> @@ -115,10 +117,6 @@ source="both" level="fatal" description="Trinity.pl not found" /> - <regex match="Error" - source="both" - level="fatal" - description="A trinity process failed" /> </stdio> <outputs> <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />