<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="3.0.3">R</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>