--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_chromosomes.xml	Wed Jun 01 03:48:29 2016 -0400
@@ -0,0 +1,84 @@
+<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>