comparison tagBed.xml @ 26:95a3b2c25bd1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59

25:e36671a0f646

        > "${output}"
]]>
    </command>
    <inputs>
        <param name="inputA" format="bam" type="data" label="BAM file"/>
        <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
        <expand macro="strand2" />
        <expand macro="overlap" />
        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
        <param name="field" type="select" label="Field from the annotation files to populate tags?">
            <option value="-labels" selected="True">Labels</option>

    </tests>
    <help>
<![CDATA[
**What it does**

Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />

26:95a3b2c25bd1

        > "${output}"
]]>
    </command>
    <inputs>
        <param name="inputA" format="bam" type="data" label="BAM file"/>
        <param name="inputB" format="@STD_BEDTOOLS_INPUTS@" multiple="True" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
        <expand macro="strand2" />
        <expand macro="overlap" />
        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
        <param name="field" type="select" label="Field from the annotation files to populate tags?">
            <option value="-labels" selected="True">Labels</option>

    </tests>
    <help>
<![CDATA[
**What it does**

Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />