comparison mapBed.xml @ 31:e19bebe96cd2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184

30:db1841942d2b

<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools map
        -a '${inputA}'
        -b '${inputB}'
        $strand
        @C_AND_O_ARGUMENT@
        -f $overlap
        $reciprocal
        $split
        $header
        @GENOME_FILE_MAPBED@
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />

        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require reciprocal overlap"
            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
        <expand macro="strand2" />
        <expand macro="c_and_o_argument">
            <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
        </expand>
        <expand macro="split" />
        <expand macro="print_header" />
        <conditional name="genome">
            <param name="genome_choose" argument="-g" type="select" 

31:e19bebe96cd2

<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
bedtools map
-a '${inputA}'
-b '${inputB}'
$strand
@C_AND_O_ARGUMENT@
-f $overlap
$reciprocal
$split
$header
@GENOME_FILE_MAPBED@
> '${output}'
]]>
    </command>
    <inputs>
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />

        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require reciprocal overlap"
            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
        <expand macro="strand2" />
        <expand macro="c_and_o_argument">
            <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
        </expand>
        <expand macro="split" />
        <expand macro="print_header" />
        <conditional name="genome">
            <param name="genome_choose" argument="-g" type="select"