diff metagene_readthrough.xml @ 11:313b8f7d2a92

(none)

--- a/metagene_readthrough.xml	Thu Jan 22 14:34:38 2015 +0100
+++ b/metagene_readthrough.xml	Thu Jan 22 14:34:53 2015 +0100
@@ -1,5 +1,5 @@
 <tool id="readthrough_analysis" name="Stop_supp">
-	<description> Analyse Ribo-seq alignment to detect readthrough events</description>
+	<description>To analyse Ribo-seq alignments for the detection of stop codon readthrough events</description>
 	<requirements>
 	    <requirement type="package">samtools</requirement>
 	    <requirement type="python-module">HTseq</requirement>
@@ -8,14 +8,15 @@
 	    <requirement type="python-module">Bio</requirement>
 	</requirements>
 	<command interpreter="python"> 
-		metagene_readthrough.py --gff $gff --fasta $fasta --bam $mapping --dirout=$output,$output.files_path
+		metagene_readthrough.py --gff $gff --fasta $fasta --bam $mapping --dirout=$output,$output.files_path --extend $ext
 
 	</command>
 
 	<inputs>
-		<param name="gff" type="data" label="References Input Annotation File (gff)" format="gff" />
-		<param name="fasta" type="data" label="Reference in fasta format" format="fasta" />
-		<param name="mapping" type="data" label="Bam Input File" format="bam" />
+		<param name="gff" type="data" label="Reference annotation file (GFF)" format="gff" />
+		<param name="fasta" type="data" label="Reference genome in Fasta format" format="fasta" />
+		<param name="mapping" type="data" label="Bam File" format="bam" />
+		<param name="ext" type="integer" label="Length of 3’ UTR extension downstream the annotated stop codon (in bp)" value="300" />
 	</inputs>
             
 	<outputs>
@@ -25,28 +26,28 @@
 	<help>
 Summary
 -------          
-This tool uses Ribo-seq data (bam file) to extract potential genes with readthrough events from a reference annotation file (GFF3).
+This tool uses Ribo-seq data (BAM file) to extract genes displaying potential stop codon readthrough events from a reference annotation file (GFF3).
 
-C-terminal protein extensions were identified as previously described (Dunn J.G. and al, 2013). Only uniquely mapped footprints whose size is in the range 25 to 34 are considered.
-A gene is read-though if :
+C-terminal protein extensions were identified as previously described (Dunn J.G. et al, 2013). Only uniquely mapped footprints with a size in the 25 to 34 range are considered.
+A gene is considered to display readthrough if:
 
  i) It is covered by more than 128 footprints.
 
- ii) There are footprints after stop codon.
+ ii) There are footprints after the stop codon.
 
- iii) There are footprints overlapping the next in frame stop codon.
+ iii) There are footprints overlapping the next in-frame stop codon.
 
- iv) There is not Methionine in the next five codons downstream the official stop codon of CDS.
+ iv) There is no methionine codon in the next five codons downstream from the official stop codon of the CDS.
 
- v) The coverage is homogeneous within the extension.
+ v) Coverage is homogeneous within the extension.
 
-Stop codon readthrough was estimated by calculating a ratio between footprints in the C-terminal extension and in the CDS. Ribosome density footprints were estimated in RPKM (reads per kilobase per million). 
-To control variability due to stop codon peaks, footprints mapping to stop codons are excluded to RPKM computing.
+Stop codon readthrough was estimated by calculating the ratio of the number of footprints in the C-terminal extension to that in the CDS. Ribosome density footprints were estimated in RPKM (reads per kilobase per million). We controlled for variability due to stop codon peaks, by excluding footprints mapping to stop codons from the calculation of RPKM.
 
+		
 Output 
 ------- 
-This tool produces html file with plots for each readthrough gene.
-
+This tool produces an html file with plots for each gene displaying readthrough.
+				
 
 Dependances
 ------------