comparison intersectBed.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_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>find overlapping intervals in various ways</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

$invert
$once
$header
$modes
@SORTED@
$bed
$count
> '${output}'
    ]]></command>
    <inputs>

        <!-- -bed -->
        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
            label="When using BAM input, write output as BED instead of BAM." />
        <!-- -sorted -g  -->
        <expand macro="sorted" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA">
            <change_format>

            <conditional name="reduce_or_iterate">
                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            </conditional>
            <param name="overlap_mode" value="-wa,-wb" />
            <param name="sorted" value="-sorted" />
            <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            <param name="inputA" value="intersect-query.bed" ftype="bed" />

                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
                <param name="names" value="yes" />
            </conditional>
            <param name="overlap_mode" value="-wa,-wb" />
            <param name="sorted" value="-sorted" />
            <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-query.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">
                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            </conditional>
            <param name="invert" value="-v" />
            <param name="sorted" value="-sorted" />
            <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-query.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">

            <param name="overlap_mode" value="-wa,-wb" />
            <conditional name="fraction_cond">
                <param name="fraction_select" value="specify"/>
                <param name="overlap" value="1.0" />
            </conditional>
            <param name="sorted" value="-sorted" />
            <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-A.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">

43:07e8b80f278c

<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>find overlapping intervals in various ways</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

$invert
$once
$header
$modes
@SORTED@
@GENOME_FILE@
$bed
$count
> '${output}'
    ]]></command>
    <inputs>

        <!-- -bed -->
        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
            label="When using BAM input, write output as BED instead of BAM." />
        <!-- -sorted -g  -->
        <expand macro="sorted" />
        <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA">
            <change_format>

            <conditional name="reduce_or_iterate">
                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            </conditional>
            <param name="overlap_mode" value="-wa,-wb" />
            <param name="sorted" value="true" />
            <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            <param name="inputA" value="intersect-query.bed" ftype="bed" />

                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
                <param name="names" value="yes" />
            </conditional>
            <param name="overlap_mode" value="-wa,-wb" />
            <param name="sorted" value="true" />
            <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-query.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">
                <param name="reduce_or_iterate_selector" value="reduce" />
                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
            </conditional>
            <param name="invert" value="-v" />
            <param name="sorted" value="true" />
            <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-query.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">

            <param name="overlap_mode" value="-wa,-wb" />
            <conditional name="fraction_cond">
                <param name="fraction_select" value="specify"/>
                <param name="overlap" value="1.0" />
            </conditional>
            <param name="sorted" value="true" />
            <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="intersect-A.bed" ftype="bed" />
            <conditional name="reduce_or_iterate">