Mercurial > repos > eganrol > rnaseqdataannotation
comparison RNAseqDataAnnotation/RNAseqDataAnnotation.xml @ 8:73ea91916c9d draft
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| author | eganrol |
|---|---|
| date | Wed, 19 Nov 2014 12:10:09 -0500 |
| parents | 22da2dc0e103 |
| children |
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| 7:80216215973c | 8:73ea91916c9d |
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| 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="3.0.2">R_3_0_2</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> |