comparison sortBed.xml @ 11:7308cc546a36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

10:c78cf6fe3018

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        sortBed 
            -i $input 
            $option 
            > $output
]]>
    </command>
    <inputs>
        <param format="bed" name="input" type="data" label="Sort the following BED file"/>
        <param name="option" type="select" label="Sort by">
            <!-- sort -k 1,1 -k2,2 -n a.bed -->
            <option value="">chromosome, then by start position (asc)</option>
            <option value="-sizeA">feature size in ascending order.</option>
            <option value="-sizeD">feature size in descending order.</option>

            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
        </param>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sortBed1.bed" ftype="bed" />
            <param name="option" value="" />

11:7308cc546a36

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        sortBed
            -i '$input'
            $option
            > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/>
        <param name="option" type="select" label="Sort by">
            <!-- sort -k 1,1 -k2,2 -n a.bed -->
            <option value="">chromosome, then by start position (asc)</option>
            <option value="-sizeA">feature size in ascending order.</option>
            <option value="-sizeD">feature size in descending order.</option>

            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
        </param>
    </inputs>
    <outputs>
        <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sortBed1.bed" ftype="bed" />
            <param name="option" value="" />