annotate complement.xml @ 5:8b6c6ec55c6e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9

<tool id="gops_complement_1" name="Complement" version="1.0.0">
    <description>intervals of a dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py"/>
    <command><![CDATA[
python '$__tool_directory__/gops_complement.py'
'$input1'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-l '${chromInfo}'
$allchroms
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Complement regions of" />
        <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement" />
    </inputs>
    <outputs>
        <data name="output" format_source="input1" metadata_source="input1" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out.bed" />
        </test>
        <test>
            <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out_diffCols.dat" />
        </test>
        <test>
            <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out2.bed" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

This operation complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input interval.

@SCREENCASTS@

**Syntax**

- **Genome-wide complement** will complement all chromosomes of the genome.  Leaving this option unchecked will only complement chromosomes present in the dataset.

-----

**Example**

.. image:: gops_complement.gif
    ]]></help>
</tool>