Mercurial > repos > eganrol > rnaseqdataannotation
comparison RNAseqDataAnnotation/RNAseqDataAnnotation.xml @ 26:f183f8648c5a draft default tip
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| author | eganrol |
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| date | Wed, 10 Dec 2014 06:42:21 -0500 |
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| 25:ea3f7a6504e0 | 26:f183f8648c5a |
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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 </requirements> | |
| 5 | |
| 6 | |
| 7 <command interpreter="R --vanilla --silent --slave -f"> | |
| 8 ./RNAseqDataAnnotation.R --args | |
| 9 $Species | |
| 10 $ensversion | |
| 11 $fileout | |
| 12 #for $i in $datafiles | |
| 13 ${i.file} | |
| 14 ${i.condition} | |
| 15 #end for | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <repeat name="datafiles" title="File" help="Upload the files to concatenate and annotate"> | |
| 20 <param name="file" label="Select file" type="data"/> | |
| 21 <param name="condition" label="Condition of the file" type="text"/> | |
| 22 </repeat> | |
| 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="hsapiens_gene_ensembl">Homo sapiens</option> | |
| 25 <option value="mmusculus_gene_ensembl">Mus musculus</option> | |
| 26 <option value="None">Other specie</option> | |
| 27 </param> | |
| 28 | |
| 29 <param name="ensversion" type="select" label="Select the version of Ensembl to use" > | |
| 30 <option value="oct2014">Version 77</option> | |
| 31 <option value="aug2014">Version 76</option> | |
| 32 <option value="feb2014">Version 75</option> | |
| 33 <option value="dec2013">Version 74</option> | |
| 34 <option value="sep2013">Version 73</option> | |
| 35 <option value="jun2013">Version 72</option> | |
| 36 <option value="apr2013">Version 71</option> | |
| 37 <option value="jan2013">Version 70</option> | |
| 38 <option value="oct2012">Version 69</option> | |
| 39 <option value="jul2012">Version 68</option> | |
| 40 <option value="may2012">Version 67</option> | |
| 41 </param> | |
| 42 </inputs> | |
| 43 | |
| 44 <outputs> | |
| 45 <data name="fileout" label="Data_normalization_annotation.txt" format="tabular"/> | |
| 46 </outputs> | |
| 47 <help> | |
| 48 **What it does** | |
| 49 This function concatenates htseq-count result files and normalizes data. | |
| 50 If the specie is known, data will be annotated using the specified Ensembl annotations. | |
| 51 | |
| 52 **How** | |
| 53 Normalization is performed using the method described in Genome Biology 2010;11(10):R106. | |
| 54 and implemented in the DESeq2 Bioconductor package. | |
| 55 Gene length correspond to the median of the size of all transcripts corresponding to this gene. | |
| 56 </help> | |
| 57 </tool> |