view makewindowsBed.xml @ 6:75d323631dce draft

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<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="0.2.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools makewindows
        #if $type.type_select == 'genome':
            -g $type.genome
        #else:
            -i $type.inputA
        #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
        #end if
        $sourcename
        &gt; $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 format="bed,vcf,gff,gff3" name="inputA" 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 (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. 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>
                 </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 (i.e. same number of windows, with varying window sizes)." />
            </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 format_source="inputA" name="output" metadata_source="inputA" label=""/>
    </outputs>
    <help>

**What it does**

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

@REFERENCES@
    </help>
</tool>