comparison sortBed.xml @ 37:ce3c7f062223 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"

36:0a5c785ac6db

    <expand macro="stdio" />
    <command><![CDATA[
sortBed
-i '$input'
$option
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
        <param name="option" type="select" label="Sort by">

            <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
            <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sortBed1.bed" ftype="bed" />
            <param name="option" value="" />
            <output name="output" file="sortBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

37:ce3c7f062223

    <expand macro="stdio" />
    <command><![CDATA[
sortBed
-i '$input'
$option
@GENOME_FILE_MAPBED@
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
        <param name="option" type="select" label="Sort by">

            <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
            <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
        </param>
        <expand macro="input_optional_genome_file" />
    </inputs>
    <outputs>
        <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sortBed1.bed" ftype="bed" />
            <param name="option" value="" />
            <output name="output" file="sortBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="sortBed2.bed" ftype="bed" />
            <param name="option" value="" />
            <output name="output" file="sortBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="sortBed2.bed" ftype="bed" />
            <param name="option" value="" />
            <param name="genome_choose" value="-g" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len" ftype="bed" />
            <output name="output" file="sortBed_result3.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**