Mercurial > repos > iuc > rnaspades
changeset 1:9e58ff014088 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit a68a0ea372748c9d7ed2c96116b7b7c4c7585af4
| author | iuc |
|---|---|
| date | Tue, 28 Mar 2017 10:53:20 -0400 |
| parents | 0d30fed9628b |
| children | 03fd468e158f |
| files | rnaspades.xml |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/rnaspades.xml Tue Dec 13 11:32:10 2016 -0500 +++ b/rnaspades.xml Tue Mar 28 10:53:20 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="rnaspades" name="rnaSPAdes" version="3.9.0"> +<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.1"> <description>assembler for RNA-Seq data</description> <requirements> <requirement type="package" version="3.9.0">spades</requirement> @@ -11,7 +11,7 @@ rnaspades.py -o . ## Forces unzipped output, faster --disable-gzip-output - $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent + $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent -k $kmer ## Sequence files, libraries #for $i, $library in enumerate( $libraries, start=1 ): #if str( $library.lib_type ) == "paired_end": @@ -54,6 +54,7 @@ <param argument="--draft-assembly" checked="False" falsevalue="" label="Draft assembly. Faster, but more error-prone" name="draft" truevalue="--draft-assembly" type="boolean" /> <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" /> <param argument="--iontorrent" checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" /> + <param argument="-k" max="127" label="k-mer size (must be odd and less than 128)" name="kmer" type="integer" value="55" /> <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries"> <param label="Library type" name="lib_type" type="select"> <option value="paired_end">Paired-end / Single reads</option>