view get_codon_frequency.xml @ 1:1fbddace2db6

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<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>