comparison fastq_dump.xml @ 18:7068f48d0ef9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"

17:c441583adae5

<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>fastq-dump --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    @SET_ACCESSIONS@

    ## Need to set the home directory to the current working directory,
    ## else the tool tries to write to home/.ncbi and fails when used
    ## with a cluster manager.
    @CONFIGURE_TIMEOUT@
    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:
        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        ## 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 ) == "" ):
            prefetch -X 200000000 "\$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"
        --split-files
    #end if
    --defline-seq '@\$sn[_\$rn]/\$ri'

    #end if


    ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" display="radio" label="Select output format" help="Compression will greatly reduce the amount of space occupied by downloaded data. Downstream applications such as a short-read mappers will accept compressed data as input. Consider this example: an uncoimpressed 400 Mb fastq datasets compresses to 100 Mb or 80 Mb by gzip or bzip2, respectively. " argument="--gzip --bzip2">
            <option value="fastqsanger.gz">gzip compressed fastq</option>
            <option value="fastqsanger">Uncompressed fastq</option>

.. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
.. _collection: https://galaxyproject.org/tutorials/collections/
.. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies

@SRATOOLS_ATTRRIBUTION@

]]>
    </help>

18:7068f48d0ef9

<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>fastq-dump --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    @COPY_CONFIGFILE@
    @SET_ACCESSIONS@

    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:
        ## 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 ) == "" ):
            prefetch -X 200000000 "\$acc" &&
        #end if
        fastq-dump --accession "\$acc"
        --split-files
    #end if
    --defline-seq '@\$sn[_\$rn]/\$ri'

    #end if


    ]]>
    </command>
    <expand macro="configfile_hack"/>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" display="radio" label="Select output format" help="Compression will greatly reduce the amount of space occupied by downloaded data. Downstream applications such as a short-read mappers will accept compressed data as input. Consider this example: an uncoimpressed 400 Mb fastq datasets compresses to 100 Mb or 80 Mb by gzip or bzip2, respectively. " argument="--gzip --bzip2">
            <option value="fastqsanger.gz">gzip compressed fastq</option>
            <option value="fastqsanger">Uncompressed fastq</option>

.. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
.. _collection: https://galaxyproject.org/tutorials/collections/
.. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies

@SRATOOLS_ATTRRIBUTION@

]]>
    </help>