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<tool id="Codon_analysis" name="Codon_density">
	<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>
	    <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="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>
				<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 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="Lenght of the best phasing footprints" value ="28"  />
		<param name="cond1" type="text" size="25" label="Condition one" help="Required even if no replicate" value="cond1"/>
		<param name="cond2" type="text" size="25" label="Condition two" help="Required even if no replicate" value="cond2"/>
		<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 can 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 can 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 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 file containing graphs and a statistical test result. An additional 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>