<tool id="get_flanks1" name="Get flanks" version="1.0.0">
    <description>returns flanking region/s for every gene</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
python '$__tool_directory__/get_flanks.py'
'$input'
'$out_file1'
$size
$direction
$region
-o $offset
-l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
    ]]></command>
    <inputs>
        <param name="input" type="data" format="interval" label="Select data"/>
        <param name="region" type="select" label="Region">
            <option value="whole" selected="true">Whole feature</option>
            <option value="start">Around Start</option>
            <option value="end">Around End</option>
        </param>
        <param name="direction" type="select" label="Location of the flanking region/s">
            <option value="Upstream">Upstream</option>
            <option value="Downstream">Downstream</option>
            <option value="Both">Both</option>
        </param>
        <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
        <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
    </inputs>
    <outputs>
        <data name="out_file1" format_source="input" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="flanks_inp.bed"/>
            <param name="offset" value="-500"/>
            <param name="size" value="1000"/>
            <param name="direction" value="Both"/>
            <param name="region" value="whole"/>
            <output name="out_file1" file="flanks_out1.bed"/>
        </test>
        <test>
            <param name="input" value="flanks_inp.bed"/>
            <param name="offset" value="200"/>
            <param name="size" value="1000"/>
            <param name="direction" value="Downstream"/>
            <param name="region" value="start" />
            <output name="out_file1" file="flanks_out2.bed"/>
        </test>
    </tests>
    <help><![CDATA[
This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.

**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".

-----

**Example 1**

- For the following dataset::

   chr22  1000  7000  NM_174568 0 +

- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::

   chr22  500  800  NM_174568 0 +

.. image:: flanks_ex1.gif

**Example 2**

- For the following dataset::

   chr22  1000  7000  NM_028946 0 -

- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::

   chr22  500  800  NM_028946 0 -

.. image:: flanks_ex2.gif
    ]]></help>
</tool>