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

Uploaded

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+++ b/RNAseqDataAnnotation/RNAseqDataAnnotation.xml	Wed Dec 10 06:42:21 2014 -0500
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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>