comparison fastq_dump.xml @ 2:f256cb398262 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026

1:462ee06c9358

<tool id="fastq_dump" name="Extract reads" version="1.3.0">
    <description>in FASTQ/A format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    #end if

    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
          [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
    #end if
    
    ## 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. 
    export HOME=\$PWD &&
    vdb-config --restore-defaults &&
    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:

    #if str( $adv.matepairDist ) != "":
        --matepair-distance "$adv.matepairDist"
    #end if
    $adv.clip
    $adv.skip_technical
    
    #if str( $outputformat ) == "fasta":
        --fasta
    #end if
    #if $input.input_select=="file":
        --stdout

    ;


    #if str( $outputformat ) == "fasta":
    
        for f in *_2.fasta ; do   mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ;  mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta"  ; done &&
        for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
        
    #else:

        for f in *_2.fastq ; do   mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ;  mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq"  ; done &&
        for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
        
    #end if





    #end if

    
    ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" label="select output format">

    </tests>
    <help>
        This tool extracts reads from SRA archives using fastq-dump.
        The fastq-dump program is developed at NCBI, and is available at
        http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
        
        NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
        @SRATOOLS_ATTRRIBUTION@
    </help>
    <expand macro="citation"/>
  </tool>

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"/>

    #end if

    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
          [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
    #end if

    ## 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.
    export HOME=\$PWD &&
    vdb-config --restore-defaults &&
    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:

    #if str( $adv.matepairDist ) != "":
        --matepair-distance "$adv.matepairDist"
    #end if
    $adv.clip
    $adv.skip_technical

    #if str( $outputformat ) == "fasta":
        --fasta
    #end if
    #if $input.input_select=="file":
        --stdout

    ;


    #if str( $outputformat ) == "fasta":

        for f in *_2.fasta ; do   mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ;  mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta"  ; done &&
        for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done

    #else:

        for f in *_2.fastq ; do   mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ;  mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq"  ; done &&
        for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done

    #end if





    #end if


    ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" label="select output format">

    </tests>
    <help>
        This tool extracts reads from SRA archives using fastq-dump.
        The fastq-dump program is developed at NCBI, and is available at
        http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.

        NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
        @SRATOOLS_ATTRRIBUTION@
    </help>
    <expand macro="citation"/>
  </tool>