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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 </requirements>
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5
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6
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7 <command interpreter="R --vanilla --silent --slave -f">
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8 ./RNAseqDataAnnotation.R --args
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9 $Species
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10 $ensversion
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11 $fileout
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12 #for $i in $datafiles
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13 ${i.file}
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14 ${i.condition}
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15 #end for
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16 </command>
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17
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18 <inputs>
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19 <repeat name="datafiles" title="File" help="Upload the files to concatenate and annotate">
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20 <param name="file" label="Select file" type="data"/>
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21 <param name="condition" label="Condition of the file" type="text"/>
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22 </repeat>
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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="hsapiens_gene_ensembl">Homo sapiens</option>
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25 <option value="mmusculus_gene_ensembl">Mus musculus</option>
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26 <option value="None">Other specie</option>
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27 </param>
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28
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29 <param name="ensversion" type="select" label="Select the version of Ensembl to use" >
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30 <option value="oct2014">Version 77</option>
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31 <option value="aug2014">Version 76</option>
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32 <option value="feb2014">Version 75</option>
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33 <option value="dec2013">Version 74</option>
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34 <option value="sep2013">Version 73</option>
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35 <option value="jun2013">Version 72</option>
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36 <option value="apr2013">Version 71</option>
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37 <option value="jan2013">Version 70</option>
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38 <option value="oct2012">Version 69</option>
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39 <option value="jul2012">Version 68</option>
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40 <option value="may2012">Version 67</option>
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41 </param>
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42 </inputs>
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43
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44 <outputs>
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45 <data name="fileout" label="Data_normalization_annotation.txt" format="tabular"/>
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46 </outputs>
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47 <help>
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48 **What it does**
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49 This function concatenates htseq-count result files and normalizes data.
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50 If the specie is known, data will be annotated using the specified Ensembl annotations.
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51
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52 **How**
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53 Normalization is performed using the method described in Genome Biology 2010;11(10):R106.
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54 and implemented in the DESeq2 Bioconductor package.
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55 Gene length correspond to the median of the size of all transcripts corresponding to this gene.
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56 </help>
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57 </tool>
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