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1 <tool id="RNAseqDataAnnotation" name="RNAseqDataAnnotation" version="1.0.0">
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2 <description>tool for RNAseq Data Normalisation and Annotation</description>
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3 <requirements>
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4 <!--<requirement type="set_environment">SCRIPT_PATH</requirement>-->
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5 <requirement type="package" version="3.0.2">R_3_0_2</requirement>
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6 <requirement type="package" version="1.0">DESeq2biomaRt</requirement>
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7 </requirements>
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8
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9 <command>
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10 R --slave --vanilla --file=RNAseqDataAnnotation.R --args
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11 $path2htseqfiles
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12 $samplenamefile
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13 $Species
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14 $ensversion
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15 $conversionensemblversion
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16 $conversionensemblname
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17 $fileout
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18 </command>
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19
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20 <inputs>
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21 <param name="path2htseqfiles" label="Path to the directory containing the files from HTSeq-count" type="text"/>
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22 <param name="samplenamefile" label="Conversion file sample/conditions" type="data" format="tabular" help="file should be tab-delimited"/>
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23 <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." >
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24 <option value="Homo_sapiens">Homo sapiens</option>
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25 <option value="Mus_musculus">Mus musculus</option>
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26 <option value="">Other specie</option>
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27 </param>
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28 <param name="ensversion" type="select" label="Select the version of Ensembl to use" >
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29 <option value="67">Version 67</option>
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30 <option value="68">Version 68</option>
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31 <option value="69">Version 69</option>
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32 <option value="70">Version 70</option>
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33 <option value="71">Version 71</option>
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34 <option value="72">Version 72</option>
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35 <option value="73">Version 73</option>
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36 <option value="74">Version 74</option>
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37 <option value="75">Version 75</option>
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38 <option value="76">Version 76</option>
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39 <option value="77">Version 77</option>
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40 </param>
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41 <param name="conversionensemblversion" label="File for conversion Ensembl to version" type="data" format="tabular" help="Tab-delimited input file" />
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42 <param name="conversionensemblname" label="File for conversion Ensemble name of the specie " type="data" format="tabular" help="Tab-delimited input file"/>
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43 </inputs>
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44
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45 <outputs>
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46 <param name="fileout" label="Path where the resulting file should be stored" type="data" format="tabular"/>
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47 </outputs>
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48 <help>
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49 **What it does*
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50 **Example**
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51 </help>
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52 </tool>
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