comparison makeWindowsBed.xml @ 35:b28e0cfa7ba1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"

34:dde39ba9c031

    #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>

            </when>
            <when value="number">
                <param name="number" argument="-n" 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" argument="-s" 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>

            <param name="type_select" value="genome" />
            <param name="genome_file_opts_selector" value="hist" />
            <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**

35:b28e0cfa7ba1

    #if $action.step_size.step_size_select == 'yes':
        -s $action.step_size.step_size
    #end if
#else:
    -n $action.number
#end if
$sourcename
> '$output'
    ]]></command>
    <inputs>

            </when>
            <when value="number">
                <param name="number" argument="-n" 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" />
            </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>

            <param name="type_select" value="genome" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <param name="action_select" value="number" />
            <param name="number" value="100" />
            <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" />
            <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**