comparison sam_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="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.10">samtools</requirement>
    </expand>
    <version_command>sam-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@
        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 $input.input_select == "file":
            sam-dump --log-level fatal  '${input.file.name}'
        #else:
            #if ( str( $adv.region ) == "" ):
                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
            sam-dump --log-level fatal --disable-multithreading
        #end if

        #if str( $adv.region ) != "":

        ) ; done
        #end if

        ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.">
            <option value="bam">bam</option>
            <option value="sam">sam</option>

@ACCESSION_LIST_HOWTO@

-----

.. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html
.. _collection: https://galaxyproject.org/tutorials/collections/
.. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies

@SRATOOLS_ATTRRIBUTION@
    ]]></help>
    <expand macro="citation"/>
</tool>

18:7068f48d0ef9

<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.10">samtools</requirement>
    </expand>
    <version_command>sam-dump --version</version_command>
    <command detect_errors="exit_code">
<![CDATA[
        @COPY_CONFIGFILE@
        @SET_ACCESSIONS@

        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.

        #if $input.input_select == "file":
            sam-dump --log-level fatal  '${input.file.name}'
        #else:
            #if ( str( $adv.region ) == "" ):
                prefetch -X 200000000 "\$acc" &&
            #end if
            sam-dump --log-level fatal --disable-multithreading
        #end if

        #if str( $adv.region ) != "":

        ) ; done
        #end if

        ]]>
    </command>
    <expand macro="configfile_hack"/>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.">
            <option value="bam">bam</option>
            <option value="sam">sam</option>

@ACCESSION_LIST_HOWTO@

-----

.. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _sam-dump: https://ncbi.github.io/sra-tools/sam-dump.html
.. _collection: https://galaxyproject.org/tutorials/collections/
.. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies

@SRATOOLS_ATTRRIBUTION@
    ]]></help>
    <expand macro="citation"/>
</tool>