# HG changeset patch
# User rlegendre
# Date 1413817599 14400
# Node ID 1fbddace2db6af1a8ed0b6c1b5cccb4316091b4b
# Parent  b8c070add3b7ab4be70e6bada6dc0e1915be7cc3
Uploaded

diff -r b8c070add3b7 -r 1fbddace2db6 get_codon_frequency.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_codon_frequency.xml	Mon Oct 20 11:06:39 2014 -0400
@@ -0,0 +1,103 @@
+<tool id="Codon_analysis" name="Codon_density">
+	<description> Analyse Ribo-seq alignments between two conditions to extract codon occupancy </description>
+	<requirements>
+	    <requirement type="package">samtools</requirement>
+	    <requirement type="python-module">matplotlib</requirement>
+	    <requirement type="python-module">numpy</requirement>
+	    <requirement type="python-module">scipy</requirement>
+	    <requirement type="python-module">Bio</requirement>
+	</requirements>
+	<command interpreter="python"> 
+		get_codon_frequency.py
+		--gff=$annot
+		--rep=$replicat_opt['rep']
+		--cond1 $cond1
+		--cond2 $cond2
+		--kmer=$kmer
+		--asite=$asite
+		--out $out
+		--site $site
+		--hex_col1 $color1
+		--hex_col2 $color2
+		--dirout $html_file,$html_file.files_path
+		#if str( $replicat_opt['rep'] ) == 'yes':
+			--file1=$file1,$file11
+			--file2=$file2,$file22
+		#else
+			--file1=$file1
+			--file2=$file2
+		#end if
+
+        
+	</command>
+
+	<inputs>
+		<param name="annot" type="data" label="References Input 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>
+				<option value="no">No</option>
+			</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" />
+			</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" />
+			</when>
+		</conditional>
+		<param name="site" type="select" label="Please choose a ribosome 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="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" />
+		<param name="color2" type="text" size="50" label="Color for second condition" value ="Plum" help="Enter standard name, hex color string, or rgb code. You cand find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html" />
+					
+	</inputs>
+
+	<outputs>
+		<data format="csv" name="out" label="Codon analysis output file on ${on_string}"/>
+		<data format="html" name="html_file" label="Codon analysis results on ${on_string}"/>
+		
+	</outputs>
+
+	<help>
+
+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.
+
+Output 
+------- 
+This tool provides an html output with graphical outputs and a statistical test result. An additionnal csv file with codon numbers is provided. 
+
+
+Dependances
+------------
+
+.. class:: warningmark
+
+This tool depends on Python (>=2.7) and following packages : numpy 1.8.0, Biopython 1.58, scipy 0.12.0 and matplotlib 1.3.1. Samtools is used for bam manipulation.
+	
+		
+		
+		
+
+
+
+
+
+	</help>
+</tool>