diff get_codon_frequency.xml @ 11:313b8f7d2a92

(none)

--- a/get_codon_frequency.xml	Thu Jan 22 14:34:38 2015 +0100
+++ b/get_codon_frequency.xml	Thu Jan 22 14:34:53 2015 +0100
@@ -1,5 +1,5 @@
 <tool id="Codon_analysis" name="Codon_density">
-	<description> Analyse Ribo-seq alignments between two conditions to extract codon occupancy </description>
+	<description>To compare Ribo-seq alignments between two sets of conditions, to determine codon occupancy </description>
 	<requirements>
 	    <requirement type="package">samtools</requirement>
 	    <requirement type="python-module">matplotlib</requirement>
@@ -32,7 +32,7 @@
 	</command>
 
 	<inputs>
-		<param name="annot" type="data" label="References Input Annotation File (gff)" format="gff" />
+		<param name="annot" type="data" label="Reference annotation file (GFF)" format="gff" />
 		<conditional name="replicat_opt">
 			<param name="rep" type="select" label="Replicate option">
 				<option value="yes">Yes (only two replicates by condition)</option>
@@ -40,23 +40,23 @@
 			</param>
 			<when value="yes">
 			## Use conditional balise : if rep =yes : 4 files, else 2 files 
-				<param name="file1" type="data" label="First replicate of first condition (bam file)" format="bam" />
-				<param name="file11" type="data" label="Second replicate of first condition (bam file)" format="bam" />
-				<param name="file2" type="data" label="First replicate of second condition (bam file)" format="bam" />
-				<param name="file22" type="data" label="First replicate of second condition (bam file)" format="bam" />
+				<param name="file1" type="data" label="First replicate of first condition (Bam file)" format="bam" />
+				<param name="file11" type="data" label="Second replicate of first condition (Bam file)" format="bam" />
+				<param name="file2" type="data" label="First replicate of second condition (Bam file)" format="bam" />
+				<param name="file22" type="data" label="First replicate of second condition (Bam file)" format="bam" />
 			</when>
 			<when value="no">
-				<param name="file1" type="data" label="First bam file" format="bam" />
-				<param name="file2" type="data" label="Second bam File" format="bam" />
+				<param name="file1" type="data" label="First Bam file" format="bam" />
+				<param name="file2" type="data" label="Second Bam File" format="bam" />
 			</when>
 		</conditional>
-		<param name="site" type="select" label="Please choose a ribosome site for codon analysis">
+		<param name="site" type="select" label="Please choose a ribosomal site for codon analysis">
 			<option value="A">A</option>
 			<option value="P">P</option>
 			<option value="E">E</option>
 		</param>
 		<param name="asite" type="integer" label="Off-set from the 5'end of the footprint to the A-site" value ="15"  />
-		<param name="kmer" type="integer" label="Size of the best phasing reads" value ="28"  />
+		<param name="kmer" type="integer" label="Lenght of the best phasing footprints" value ="28"  />
 		<param name="cond1" type="text" size="25" label="Condition one" help="Required even if no replicate" />
 		<param name="cond2" type="text" size="25" label="Condition two" help="Required even if no replicate" />
 		<param name="color1" type="text" size="50" label="Color for first condition" value ="SkyBlue" help="Enter standard name, hex color string, or rgb code. You cand find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html" />
@@ -74,14 +74,12 @@
 
 Summary
 -------   
-This tool uses Ribo-seq (bam file) to compare codon translation between two conditions.
-For each footprint, codons at choosen site are saved and an histogram with all normalized codon numbers is plotted in both conditions. 
-A second histogram groups all codons corresponding to an amino acid.
-A chisquare test is used for testing if distribution of used codons is the same in both conditions.
+This tool uses Ribo-seq (BAM file) to determine whether codon occupancy differs between two sets of conditions. For each footprint, the codons at the chosen site are recorded and a histogram displaying all the normalised codon numbers is plotted for both sets of conditions. A second histogram groups together all the codons corresponding to a given amino acid. A chi-squared test is then carried out to determine whether the distribution of the codons used is the same in both sets of conditions.
+
 
 Output 
 ------- 
-This tool provides an html output with graphical outputs and a statistical test result. An additionnal csv file with codon numbers is provided. 
+This tool provides an html file containing graphs and a statistical test result. An additional csv file with codon numbers is provided. 
 
 
 Dependances