comparison mapBed.xml @ 43:07e8b80f278c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"

42:841fb4dc3ab3

<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

    -F $overlapB
#end if
$reciprocal
$split
$header
@GENOME_FILE_MAPBED@
> '${output}'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />

        <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" />
        <expand macro="input_optional_genome_file" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
    </outputs>
    <tests>

            <repeat name="c_and_o_argument_repeat">
                <param name="col" value="5" />
                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <param name="genome_choose" value="-g" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len" ftype="bed" />
            <output name="output" file="mapBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

43:07e8b80f278c

<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.3" profile="@PROFILE@">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

    -F $overlapB
#end if
$reciprocal
$split
$header
@GENOME_FILE@
> '${output}'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />

        <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" />
        <expand macro="input_conditional_genome_file" optional="true"/>
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
    </outputs>
    <tests>

            <repeat name="c_and_o_argument_repeat">
                <param name="col" value="5" />
                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <conditional name="genome_file_opts">
                <param name="genome_file_opts_selector" value="hist" />
                <param name="genome" value="mm9.len" ftype="bed" />
            </conditional>
            <output name="output" file="mapBed_result5.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="mapBed3.bed" ftype="bed" />
            <param name="inputB" value="mapBed4.bed" ftype="bed" />
            <repeat name="c_and_o_argument_repeat">
                <param name="col" value="5" />
                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <conditional name="genome_file_opts">
                <param name="genome_file_opts_selector" value="loc" />
                <param name="genome" value="mm9"/>
            </conditional>
            <output name="output" file="mapBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**