Mercurial > repos > iuc > rnaspades
comparison rnaspades.xml @ 2:03fd468e158f draft
"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 |
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| 1:9e58ff014088 | 2:03fd468e158f |
|---|---|
| 6 <stdio> | 6 <stdio> |
| 7 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
| 8 </stdio> | 8 </stdio> |
| 9 <command> | 9 <command> |
| 10 <![CDATA[ | 10 <![CDATA[ |
| 11 | |
| 12 if [[ -n \$GALAXY_MEMORY_MB ]]; then | |
| 13 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); | |
| 14 fi && | |
| 15 | |
| 11 rnaspades.py -o . | 16 rnaspades.py -o . |
| 12 ## Forces unzipped output, faster | 17 ## Forces unzipped output, faster |
| 13 --disable-gzip-output | 18 --disable-gzip-output |
| 14 $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent -k $kmer | 19 $draft $onlyassembler -t \${GALAXY_SLOTS:-4} -m \${GALAXY_MEMORY_GB:-250} $iontorrent -k $kmer |
| 15 ## Sequence files, libraries | 20 ## Sequence files, libraries |
| 16 #for $i, $library in enumerate( $libraries, start=1 ): | 21 #for $i, $library in enumerate( $libraries, start=1 ): |
| 17 #if str( $library.lib_type ) == "paired_end": | 22 #if str( $library.lib_type ) == "paired_end": |
| 18 #set prefix = 'pe' | 23 #set prefix = 'pe' |
| 19 #elif str( $library.lib_type ) == "mate_paired": | 24 #elif str( $library.lib_type ) == "mate_paired": |