annotate makeWindowsBed.xml @ 1:82aac94b06c3 draft

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<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools makewindows
        #if $type.type_select == 'genome':
            -g $type.genome
        #else:
            -b $type.input
        #end if
        #if $action.action_select == 'windowsize':
            -w $action.windowsize
            #if $action.step_size.step_size_select == 'yes':
                -s $action.step_size.step_size
            #end if
        #else:
            -n $action.number
            -s $action.step_size
        #end if
        $sourcename
        > $output
]]>
    </command>
    <inputs>
         <conditional name="type">
            <param name="type_select" type="select" label="Work with">
                <option value="bed" selected="True">Bed File</option>
                <option value="genome">Genome File</option>
            </param>
            <when value="bed">
                <param  name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/>
            </when>
            <when value="genome">
                <expand macro="genome" />
            </when>
        </conditional>
        <conditional name="action">
            <param name="action_select" type="select" label="Work with">
                <option value="windowsize" selected="True">Set WindowSize</option>
                <option value="number">Give Number of Windows</option>
            </param>
            <when value="windowsize">
                <param name="windowsize" type="integer" value="1"
                    label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
                    help="i.e. same number of nucleotide in each window" />
                 <conditional name="step_size">
                    <param name="step_size_select" type="select"
                        label="Specify Step size? i.e. how many base pairs to step before creating a new window"
                        help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
                        <option value="yes">Yes</option>
                        <option value="no" selected="True">No</option>
                    </param>
                    <when value="yes">
                        <param name="step_size" type="integer" value="100" label="Specify it" />
                    </when>
                    <when value="no" />
                 </conditional>
            </when>
            <when value="number">
                <param name="number" type="integer" value="1"
                    label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
                    help="i.e. same number of windows, with varying window sizes" />
                <param name="step_size" type="integer" value="100" label="Specify it" />
            </when>
        </conditional>
        <param name="sourcename" type="select" label="ID Naming Options">
            <option value="" selected="True">Default</option>
            <option value="-i src">use the source interval's name</option>
            <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
            <option value="-i srcwinnum">use the source interval's name with the window number.</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="type_select" value="genome" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <param name="action_select" value="windowsize" />
            <param name="windowsize" value="1000000" />
            <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="type_select" value="genome" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <param name="action_select" value="windowsize" />
            <param name="windowsize" value="1000000" />
            <param name="step_size_select" value="yes" />
            <param name="step_size" value="50000" />
            <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="type_select" value="genome" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <param name="action_select" value="number" />
            <param name="number" value="100" />
            <param name="step_size" value="10000" />
            <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
        </test>
        <test>
            <param name="type_select" value="bed" />
            <param name="input" value="makeWindowBed1.bed" ftype="bed" />
            <param name="action_select" value="number" />
            <param name="number" value="15" />
            <param name="step_size" value="100" />
            <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Makes adjacent or sliding windows across a genome or BED file.

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