# HG changeset patch
# User iuc
# Date 1490712800 14400
# Node ID 9e58ff0140880d8bd4303b95c396eba0d8c4a110
# Parent  0d30fed9628b3cc8c1d566843ec79c65a8542068
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit a68a0ea372748c9d7ed2c96116b7b7c4c7585af4

diff -r 0d30fed9628b -r 9e58ff014088 rnaspades.xml
--- 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>