Mercurial > repos > iuc > trinity
diff trinity.xml @ 2:de0af39266ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
| author | iuc |
|---|---|
| date | Mon, 25 Apr 2016 10:02:37 -0400 |
| parents | 0067c78f49dc |
| children | c7555bc21812 |
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--- a/trinity.xml Wed Dec 09 07:19:52 2015 -0500 +++ b/trinity.xml Mon Apr 25 10:02:37 2016 -0400 @@ -1,7 +1,7 @@ -<tool id="trinity" name="Trinity" version="2.0.6.1"> +<tool id="trinity" name="Trinity" version="2.1.1"> <description>de novo assembly of RNA-Seq data</description> <requirements> - <requirement type="package" version="2.0.6">trinity</requirement> + <requirement type="package" version="2.1.1">trinity</requirement> <requirement type="package" version="1.1.2">bowtie</requirement> <requirement type="package" version="1.2">samtools</requirement> <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> @@ -62,9 +62,9 @@ #end if ## CPU and butterfly options. - --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr" + --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" - > $trinity_log 2>&1 + ## > $trinity_log 2>&1 ]]></command> <inputs> @@ -87,11 +87,10 @@ </param> </when> </conditional> - <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/> <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/> </when> <when value="single"> - <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -130,7 +129,7 @@ </section> </inputs> <outputs> - <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> + <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /--> <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> </outputs> <tests>