view RNAseqDataAnnotation/RNAseqDataAnnotation.xml @ 26:f183f8648c5a draft default tip

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<tool id="RNAseqDataAnnotation" name="RNAseqDataAnnotation" version="1.0.0">
  <description>tool for RNAseq Data Normalisation and Annotation</description>
  <requirements>
  </requirements>


  <command interpreter="R --vanilla --silent --slave -f">
./RNAseqDataAnnotation.R --args 
	$Species
	$ensversion
	$fileout
	#for $i in $datafiles
        ${i.file}
        ${i.condition}
    #end for
 </command>

  <inputs>
      <repeat name="datafiles" title="File" help="Upload the files to concatenate and annotate">
      <param name="file" label="Select file" type="data"/>
      <param name="condition" label="Condition of the file" type="text"/>
      </repeat>
	  <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." >
		<option value="hsapiens_gene_ensembl">Homo sapiens</option>
		<option value="mmusculus_gene_ensembl">Mus musculus</option> 
		<option value="None">Other specie</option>
	  </param>
	  
	  <param name="ensversion" type="select" label="Select the version of Ensembl to use" >
		<option value="oct2014">Version 77</option>
		<option value="aug2014">Version 76</option>
		<option value="feb2014">Version 75</option>
		<option value="dec2013">Version 74</option>
		<option value="sep2013">Version 73</option>
		<option value="jun2013">Version 72</option>
		<option value="apr2013">Version 71</option>
		<option value="jan2013">Version 70</option>
		<option value="oct2012">Version 69</option>
		<option value="jul2012">Version 68</option> 
		<option value="may2012">Version 67</option>
	  </param>
  </inputs>

  <outputs>
  <data name="fileout" label="Data_normalization_annotation.txt" format="tabular"/>  
  </outputs>
 <help>
**What it does**
	This function concatenates htseq-count result files and normalizes data.
	If the specie is known, data will be annotated using the specified Ensembl annotations.

**How**
	Normalization is performed using the method described in Genome Biology 2010;11(10):R106. 
	and implemented in the DESeq2 Bioconductor package.
	Gene length correspond to the median of the size of all transcripts corresponding to this gene.
 </help>
 </tool>