comparison fastq_dump.xml @ 3:4732693f4661 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd

2:f256cb398262

<tool id="fastq_dump" name="Extract reads" version="2.6.2">
    <description>in FASTQ/A format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.
        #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
            ASCP_PATH=`command -v ascp` &&
            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
            ## Duplicate vdb-config, in case settings changed between prefetch and
            ## dump command.
            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        #end if
        fastq-dump --accession "\$acc"

3:4732693f4661

<tool id="fastq_dump" name="Extract reads" version="@VERSION@">
    <description>in FASTQ/A format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.
        #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
            ASCP_PATH=`command -v ascp` &&
            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
            ## Duplicate vdb-config, in case settings changed between prefetch and
            ## dump command.
            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        #end if
        fastq-dump --accession "\$acc"