Mercurial > repos > nate > trinity_psc
changeset 2:53b890343b67 draft
Uploaded
| author | nate |
|---|---|
| date | Mon, 26 Sep 2016 16:09:24 -0400 |
| parents | 976e99dd3c2b |
| children | 3d072b99688e |
| files | trinityrnaseq.xml |
| diffstat | 1 files changed, 9 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/trinityrnaseq.xml Fri Sep 23 10:01:55 2016 -0400 +++ b/trinityrnaseq.xml Mon Sep 26 16:09:24 2016 -0400 @@ -14,16 +14,20 @@ <command> MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ; - workdir=`pwd`; + workdir=`pwd`; echo "workdir is \$workdir"; - cd \$LOCAL; - echo "Running Trinity from `pwd`"; + cd \$LOCAL; + echo "Running Trinity from `pwd`"; Trinity --max_memory "\${MEM}G" --CPU "\${GALAXY_SLOTS:-16}" --bflyHeapSpaceMax "32G" --bflyHeapSpaceInit "2G" --bflyGCThreads "6" + + #if $additional_params.use_additional == "yes" and $additional_params.normalize_reads == "yes": + --normalize_reads + #end if ## Inputs. #if str($inputs.paired_or_single) == "paired": @@ -111,6 +115,8 @@ <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" /> <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" /> <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> + <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> + <param name="normalize_reads" type="boolean" truevalue="yes" falsevalue="no" help="(--normalize_reads) Normalize reads, can decrease runtime and memory requirements for datasets exceeding 300M pairs"/> </when> </conditional> </inputs>