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comparison spades.xml @ 8:884dc0264950 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e
author iuc
date Fri, 21 Sep 2018 17:42:09 -0400
parents 9006e5836729
children 24fffa4fee40
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7:9006e5836729 8:884dc0264950
1 <tool id="spades" name="SPAdes" version="3.11.1"> 1 <tool id="spades" name="SPAdes" version="3.11.1+galaxy1">
2 <description>genome assembler for regular and single-cell projects</description> 2 <description>genome assembler for regular and single-cell projects</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.11.1">spades</requirement> 4 <requirement type="package" version="3.11.1">spades</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 <regex match="The reads contain too many k-mers to fit into available memory"
9 source="stdout"
10 level="fatal_oom"
11 description="Out of memory error occurred" />
8 </stdio> 12 </stdio>
9 <command> 13 <command>
10 <![CDATA[ 14 <![CDATA[
11 ## 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 15 ## 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
12 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} 16 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}