comparison mergeBed.xml @ 1:82aac94b06c3 draft

Uploaded

0:b8348686a0b9

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        mergeBed 
            -i $input
            $strandedness
            $report_number
            -d $distance
            $nms
            #if str($scores) != 'none'
                -scores $scores
            #end if
            &gt; $output
    </command>
    <inputs>
        <param  name="input" format="bed,gff,vcf" type="data" label="Sort the following BED/VCF/GFF file"/>
        <param name="strandedness" type="boolean" label="Force strandedness." truevalue="-s" falsevalue="" checked="false" 
            help="That is, only merge features that are the same strand."/>
        <param name="report_number" type="boolean" label="Report the number of BED entries that were merged." truevalue="-n" falsevalue="" checked="false" 
            help="1 is reported if no merging occurred."/>
        <param name="nms" type="boolean" label="Report the names of the merged features separated by commas." truevalue="-nms" falsevalue="" checked="false" 
            help="1 is reported if no merging occurred."/>

        <param name="distance" type="integer" value="0" label="Maximum distance between features allowed for features to be merged." 
            help="That is, overlapping and/or book-ended features are merged."/>
        <param name="scores" type="select" label="Report the scores of the merged features as">
            <option value="none" selected="True">Do not report at all</option>
            <option value="sum">Sum</option>
            <expand macro="math_options" />
        </param>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="0.bed" ftype="bed" />
            <output name="output" file="0_result.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="1.bed" ftype="bed" />
            <param name="strandedness" value="-s" />
            <output name="output" file="1_result.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="2.bed" ftype="bed" />
            <param name="report_number" value="-n" />
            <output name="output" file="2_result.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="3.bed" ftype="bed" />
            <param name="distance" value="1000" />
            <output name="output" file="3_result.bed" ftype="bed" />
        </test>
    </tests>
    <help>

**What it does**

bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.

  chr1  100  500  3

  $ bedtools merge -i A.bed -scores collapse
  chr1  100  500  1,2,3


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

1:82aac94b06c3

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        mergeBed
            -i "${input}"
            $strand
            -d $distance
            $header
            > "${output}"
]]>
    </command>
    <inputs>
        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
        <param name="strand" type="select" label="Calculation based on strandedness?">
            <option value="" selected="True">Overlaps on either strand</option>
            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
            <option value="-S +">Force merge for forward strand only.</option>
            <option value="-S -">Force merge for reverse strand only.</option>
        </param>
        <param name="distance" type="integer" value="0"
            label="Maximum distance between features allowed for features to be merged"
            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
        <expand macro="print_header" />
        <expand macro="choose_columns" />
        <expand macro="choose_operations">
            <expand macro="math_options" />
            <expand macro="additional_math_options" />
        </expand>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="mergedBed1.bed" ftype="bed" />
            <output name="output" file="mergedBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed2.bed" ftype="bed" />
            <param name="strandedness" value="-s" />
            <output name="output" file="mergedBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed3.bed" ftype="bed" />
            <param name="report_number" value="-n" />
            <output name="output" file="mergedBed_result3.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed4.bed" ftype="bed" />
            <param name="distance" value="1000" />
            <output name="output" file="mergedBed_result4.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.

  chr1  100  500  3

  $ bedtools merge -i A.bed -scores collapse
  chr1  100  500  1,2,3

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