--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNAseqDataAnnotation/RNAseqDataAnnotation.xml	Wed Nov 19 12:10:09 2014 -0500
@@ -0,0 +1,52 @@
+<tool id="RNAseqDataAnnotation" name="RNAseqDataAnnotation" version="1.0.0">
+  <description>tool for RNAseq Data Normalisation and Annotation</description>
+  <requirements>
+    <!--<requirement type="set_environment">SCRIPT_PATH</requirement>-->
+    <requirement type="package" version="3.0.2">R_3_0_2</requirement>
+    <requirement type="package" version="1.0">DESeq2biomaRt</requirement>
+  </requirements>
+
+ <command>
+	R --slave --vanilla --file=RNAseqDataAnnotation.R --args 
+	$path2htseqfiles
+	$samplenamefile
+	$Species
+	$ensversion
+	$conversionensemblversion
+	$conversionensemblname
+	$fileout
+ </command>
+
+  <inputs>
+	  <param name="path2htseqfiles" label="Path to the directory containing the files from HTSeq-count" type="text"/>
+	  <param name="samplenamefile" label="Conversion file sample/conditions" type="data" format="tabular" help="file should be tab-delimited"/>
+	  <param name="Species" type="select" label="Select the specie for your data" help="If your specie of interest is not listed, your data will be normalized but no annotation will be added. Contact us if you want us to add your specie." >
+		<option value="Homo_sapiens">Homo sapiens</option>
+		<option value="Mus_musculus">Mus musculus</option> 
+		<option value="">Other specie</option>
+	  </param>
+	  <param name="ensversion" type="select" label="Select the version of Ensembl to use" >
+		<option value="67">Version 67</option>
+		<option value="68">Version 68</option> 
+		<option value="69">Version 69</option>
+		<option value="70">Version 70</option>
+		<option value="71">Version 71</option> 
+		<option value="72">Version 72</option>
+		<option value="73">Version 73</option>
+		<option value="74">Version 74</option> 
+		<option value="75">Version 75</option>
+		<option value="76">Version 76</option>
+		<option value="77">Version 77</option>
+	  </param>
+	  <param name="conversionensemblversion" label="File for conversion Ensembl to version" type="data" format="tabular" help="Tab-delimited input file" />
+	  <param name="conversionensemblname" label="File for conversion Ensemble name of the specie " type="data" format="tabular" help="Tab-delimited input file"/>
+  </inputs>
+
+  <outputs>
+<param name="fileout" label="Path where the resulting file should be stored" type="data" format="tabular"/>  
+  </outputs>
+ <help>
+**What it does*
+**Example**
+ </help>
+ </tool>