--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyCalculateChromosomeLengths.xml	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,53 @@
+<tool id="pyCalculateChromosomeLengths" name="pyCalculateChromosomeLengths">
+	  <requirements>
+        	<requirement type="package">pyCRAC</requirement>
+    	  </requirements>
+ 	  <command interpreter="python">
+	  /usr/local/bin/pyCalculateChromosomeLengths.py 
+	  -f $ftype.input 
+	  --file_type $ftype.filetype 
+	  -o $output </command>
+	  <version_command>/usr/local/bin/pyCalculateChromosomeLengths.py --version</version_command>
+ 	  <inputs>
+	      <conditional name="ftype">
+	      <param name="filetype" type="select"  label="File type">
+                                        <option value="fasta" selected="true">Fasta</option>
+                                        <option value="tab">Tab</option>
+	      </param>        
+	      <when value="fasta">
+		              <param name="input" type="data" format="fasta" label="Input file" help="Fasta or Tab file"/>
+	      </when>
+	      <when value="tab">
+                              <param name="input" type="data" format="tabular" label="Input file" help="Fasta or Tab file"/>
+	      </when>
+	      </conditional>
+ 	  </inputs>
+	  <param name="label" type="text" format="txt" size="30" value="pyCalculateChromosomeLengths" label="Enter output file label -o" />
+ 	  <outputs>
+	    <data name="output" format="txt" label="${label.value}.len"/>
+ 	  </outputs>
+	  <help>
+
+.. class:: infomark
+
+**pyCalculateChromosomeLengths**
+
+pyCalculateChromosomeLengths is part of the pyCRAC_ package. Takes a genome sequence in fasta or tab format and generates a tab-delimited file showing chromosome name and chromosome length.
+   
+.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
+
+-------
+
+**Parameter list**                                                                     
+
+Options::
+
+  -f chromosomes.fasta, --input_file=chromosomes.fasta
+                        provide the name and path of your fasta or tab genomic
+                        sequence file. Default is standard input.
+  --file_type=fasta     
+                        provide the file type (fasta or tab). Default is fasta
+
+ 	  </help>
+</tool>
+