comparison spades.xml @ 8:884dc0264950 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e

7:9006e5836729

<tool id="spades" name="SPAdes" version="3.11.1">
    <description>genome assembler for regular and single-cell projects</description>
    <requirements>
        <requirement type="package" version="3.11.1">spades</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
    <![CDATA[
    ## 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 $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}

8:884dc0264950

<tool id="spades" name="SPAdes" version="3.11.1+galaxy1">
    <description>genome assembler for regular and single-cell projects</description>
    <requirements>
        <requirement type="package" version="3.11.1">spades</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <regex match="The reads contain too many k-mers to fit into available memory"
           source="stdout"
           level="fatal_oom"
	   description="Out of memory error occurred" />
    </stdio>
    <command>
    <![CDATA[
    ## 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 $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}