Mercurial > repos > nml > metaspades
comparison metaspades.xml @ 5:3ca2d2a9068c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
author | iuc |
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date | Thu, 16 Sep 2021 15:25:29 +0000 |
parents | ce02f513e598 |
children | a9b8c9e204ee |
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4:ce02f513e598 | 5:3ca2d2a9068c |
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1 <tool id="metaspades" name="metaSPAdes" version="3.9.0.1"> | 1 <tool id="metaspades" name="metaSPAdes" version="3.9.0.1"> |
2 <description>assembler for metagenomics datasets</description> | 2 <description>assembler for metagenomics datasets</description> |
3 <xrefs> | |
4 <xref type="bio.tools">metaspades</xref> | |
5 </xrefs> | |
3 <requirements> | 6 <requirements> |
4 <requirement type="package" version="3.9.0">spades</requirement> | 7 <requirement type="package" version="3.9.0">spades</requirement> |
5 </requirements> | 8 </requirements> |
6 <stdio> | 9 <stdio> |
7 <exit_code range="1:" /> | 10 <exit_code range="1:" /> |
8 </stdio> | 11 </stdio> |
9 <command> | 12 <command> |
10 <![CDATA[ | 13 <![CDATA[ |
11 | 14 |
12 if [[ -n \$GALAXY_MEMORY_MB ]]; then | 15 if [ -n "\$GALAXY_MEMORY_MB" ]; then |
13 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); | 16 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); |
14 fi && | 17 fi && |
15 | 18 |
16 ## 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 | 19 ## 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 |
17 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} | 20 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} |