Mercurial > repos > nml > metaspades

diff metaspades.xml @ 3:2ecf5a570907 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
author iuc
date Fri, 15 Jan 2021 12:28:26 +0000
parents 05c394313b1c
children ce02f513e598
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line diff
--- a/metaspades.xml	Tue Nov 06 12:21:15 2018 -0500
+++ b/metaspades.xml	Fri Jan 15 12:28:26 2021 +0000
@@ -8,8 +8,13 @@
     </stdio>
     <command>
     <![CDATA[
+
+    if [[ -n \$GALAXY_MEMORY_MB ]]; then
+        GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
+    fi &&
+
     ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
-    spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16}
+    spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
     #if not $kmer_choice.auto_kmer_choice:
         -k "$kmer_choice.kmers"
     #end if