comparison tagBed.xml @ 1:82aac94b06c3 draft

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0:b8348686a0b9

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools tag
        -i $inputA
        -files 
        #for $bed in beds:
            $bed.input
        #end for
        -f $overlap
        $strand
        -tag $tag
        $field
        &gt; $output
    </command>
    <inputs>
        <param format="bam" name="inputA" type="data" label="BAM file"/>

        <repeat name="beds" title="Add files" >
            <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" />
        </repeat>
        <expand macro="strand2" />
        <expand macro="overlap" />
        
        <param name="tag" type="text" value="YB" label="Dictate what the tag should be." />
        <param name="field" type="select" label="Use which field from the annotation files to populate tags?">
            <option value="-labels" selected="True">labels</option>
            <option value="-scores">Scores</option>
            <option value="-names">Names</option>
            <option value="-labels -intervals">Intervals</option>
        </param>
    </inputs>
    <outputs>
        <data format="bed" name="output" label="" />
    </outputs>
    <help>
    
**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" />
</tool>

1:82aac94b06c3

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
        bedtools tag
        -i "${inputA}"
        -files "${files}"
        -f $overlap
        $strand
        -tag "${tag}"
        $field
        > "${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>
            <option value="-scores">Scores</option>
            <option value="-names">Names</option>
            <option value="-labels -intervals">Intervals</option>
        </param>
    </inputs>
    <outputs>
        <data format="bam" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="srma_in3.bam" ftype="bam" />
            <param name="inputB" value="tagBed1.bed" ftype="bed" />
            <param name="field" value="-names" />
            <output name="output" file="tagBed_result1.bam" ftype="bam" />
        </test>
    </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" />
</tool>