comparison fasterq_dump.xml @ 36:1ec814014652 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb

35:de0f7e0a3896

<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>format from NCBI SRA</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <version_command>fasterq-dump --version | tr -d $'\n'</version_command>

    set -o | grep -q pipefail && set -o pipefail;
    @COPY_CONFIGFILE@
    @CONFIGURE_RETRY@
    @SET_ACCESSIONS@
    while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
        --seq-defline '$adv.seq_defline'
        --qual-defline '+'
        $adv.split
        #if str( $adv.minlen ) != "":
            --min-read-len "$adv.minlen"

36:1ec814014652

<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>format from NCBI SRA</description>
    <macros>
        <import>macros.xml</import>
        <token name="VERSION_SUFFIX">1</token>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <version_command>fasterq-dump --version | tr -d $'\n'</version_command>

    set -o | grep -q pipefail && set -o pipefail;
    @COPY_CONFIGFILE@
    @CONFIGURE_RETRY@
    @SET_ACCESSIONS@
    while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
        fasterq-dump "\$acc"
        -e \${GALAXY_SLOTS:-1}
        -t \${TMPDIR}
        --seq-defline '$adv.seq_defline'
        --qual-defline '+'
        $adv.split
        #if str( $adv.minlen ) != "":
            --min-read-len "$adv.minlen"