|
0
|
1 <tool id="RNAseqDataAnnotation" name="RNAseqDataAnnotation" version="1.0.0">
|
|
|
2 <description>tool for RNAseq Data Normalisation and Annotation</description>
|
|
|
3 <requirements>
|
|
|
4 <!--<requirement type="set_environment">SCRIPT_PATH</requirement>-->
|
|
|
5 <requirement type="package" version="3.0.3">R</requirement>
|
|
|
6 <requirement type="package" version="1.0">DESeq2biomaRt</requirement>
|
|
|
7 </requirements>
|
|
|
8
|
|
|
9 <command>
|
|
|
10 R --slave --vanilla --file=RNAseqDataAnnotation.R --args
|
|
|
11 $path2htseqfiles
|
|
|
12 $samplenamefile
|
|
|
13 $Species
|
|
|
14 $ensversion
|
|
|
15 $conversionensemblversion
|
|
|
16 $conversionensemblname
|
|
|
17 $fileout
|
|
|
18 </command>
|
|
|
19
|
|
|
20 <inputs>
|
|
|
21 <param name="path2htseqfiles" label="Path to the directory containing the files from HTSeq-count" type="text"/>
|
|
|
22 <param name="samplenamefile" label="Conversion file sample/conditions" type="data" format="tabular" help="file should be tab-delimited"/>
|
|
|
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." >
|
|
|
24 <option value="Homo_sapiens">Homo sapiens</option>
|
|
|
25 <option value="Mus_musculus">Mus musculus</option>
|
|
|
26 <option value="">Other specie</option>
|
|
|
27 </param>
|
|
|
28 <param name="ensversion" type="select" label="Select the version of Ensembl to use" >
|
|
|
29 <option value="67">Version 67</option>
|
|
|
30 <option value="68">Version 68</option>
|
|
|
31 <option value="69">Version 69</option>
|
|
|
32 <option value="70">Version 70</option>
|
|
|
33 <option value="71">Version 71</option>
|
|
|
34 <option value="72">Version 72</option>
|
|
|
35 <option value="73">Version 73</option>
|
|
|
36 <option value="74">Version 74</option>
|
|
|
37 <option value="75">Version 75</option>
|
|
|
38 <option value="76">Version 76</option>
|
|
|
39 <option value="77">Version 77</option>
|
|
|
40 </param>
|
|
|
41 <param name="conversionensemblversion" label="File for conversion Ensembl to version" type="data" format="tabular" help="Tab-delimited input file" />
|
|
|
42 <param name="conversionensemblname" label="File for conversion Ensemble name of the specie " type="data" format="tabular" help="Tab-delimited input file"/>
|
|
|
43 </inputs>
|
|
|
44
|
|
|
45 <outputs>
|
|
|
46 <param name="fileout" label="Path where the resulting file should be stored" type="data" format="tabular"/>
|
|
|
47 </outputs>
|
|
|
48 <help>
|
|
|
49 **What it does*
|
|
|
50 **Example**
|
|
|
51 </help>
|
|
|
52 </tool>
|
