Mercurial > repos > iuc > rnaspades

changeset 2:03fd468e158f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit b7a410ba698811d0b903b3c72191ae6564bf5a8c"
author iuc
date Thu, 07 Jan 2021 17:50:06 +0000
parents 9e58ff014088
children a8a278849c18
files rnaspades.xml
diffstat 1 files changed, 6 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/rnaspades.xml	Tue Mar 28 10:53:20 2017 -0400
+++ b/rnaspades.xml	Thu Jan 07 17:50:06 2021 +0000
@@ -8,10 +8,15 @@
     </stdio>
     <command>
         <![CDATA[
+
+        if [[ -n \$GALAXY_MEMORY_MB ]]; then
+            GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
+        fi &&
+
         rnaspades.py -o .
         ## Forces unzipped output, faster
         --disable-gzip-output
-        $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent -k $kmer
+        $draft $onlyassembler -t \${GALAXY_SLOTS:-4} -m \${GALAXY_MEMORY_GB:-250} $iontorrent -k $kmer
         ## Sequence files, libraries
         #for $i, $library in enumerate( $libraries, start=1 ):
             #if str( $library.lib_type ) == "paired_end":