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comparison metaspades.xml @ 5:3ca2d2a9068c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
author iuc
date Thu, 16 Sep 2021 15:25:29 +0000
parents ce02f513e598
children a9b8c9e204ee
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4:ce02f513e598 5:3ca2d2a9068c
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}