<tool id="map_chromosomes" name="Convert between UCSC and ensembl chromosome names" version="0.0.1">
    <description>chromosome representation</description>
    <command  interpreter="perl">map_chromosomes.pl $input1 $col $delimiter ${map.fields.path} $out_file1</command>
    <inputs>
        <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
        <param name="col" type="integer" value="1" label="Column containing chromosome ids"/>
        <param name="delimiter" type="select" label="Delimited by">
            <option value="TAB">Tab</option>
            <option value="SPACE">Whitespace</option>
            <option value="DOT">Dot</option>
            <option value="COMMA">Comma</option>
            <option value="DASH">Dash</option>
            <option value="UNDERSCORE">Underscore</option>
            <option value="PIPE">Pipe</option>
        </param>
        <param name="map" type="select" label="Select a mapping file" help="Ensure you select the correct mapping file">
            <options from_data_table="map_chromosomes">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="out_file1" format="input" metadata_source="input1"/>
    </outputs>

    <tests>
	<test>
		<param name="col" value="1"/>
		<param name="delimiter" value="TAB"/>
		<param name="map" value="hg19 UCSC to ensembl"/>
		<param name="input1" value="map_chrom_ucsc.txt" dbkey="hg19" />
		<output name="out_file1" file="map_chrom_ensembl.txt"/>
    	</test>
        <test>
                <param name="col" value="1"/>
                <param name="delimiter" value="TAB"/>
                <param name="map" value="hg19 ensembl to UCSC"/>
                <param name="input1" value="map_chrom_ensembl.txt" dbkey="hg19" />
                <output name="out_file1" file="map_chrom_ucsc.txt"/>
        </test>
    </tests>
    <help>


**What it does**

Converts a column between the UCSC and ensembl representation of chromosomes.

.. class:: warningmark

**Warning any lines containing chromosomes that don't map or are invalid will be removed**

-----

**Example 1**

Converting this dataset::

  chr21 12      123
  chrM  45      345

by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 UCSC to ensembl** will produce::

  21    12      123
  MT    45      345

-----

**Example 2**

Converting this dataset::

  21    12      123
  MT    45      345

by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 ensembl to UCSC** will produce::

  chr21 12      123
  chrM  45      345


    </help>
</tool>