view kmer_analysis.xml @ 19:385fc64fa988 draft default tip

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<tool id="kmer_analysis" name="Kmer">
	<description>To calculate the proportion and phasing of each kmer</description>
	<requirements>
		<requirement type="package">samtools</requirement>
	    <requirement type="package">numpy</requirement>
        <requirement type="package">matplotlib</requirement>
        <requirement type="package">pysam</requirement>
	</requirements>
	<command interpreter="python"> 
		kmer_analysis.py --gff $gff --bam $bamfile --dirout $output.files_path --out $output
 
	</command>

	<inputs>
		<param name="gff" type="data" label="Reference annotation file (GFF))" format="gff" />
		<param name="bamfile" type="data" label="Bam file" format="bam" />
	</inputs>

	<outputs>
		<data format="html" name="output" label="Kmer report on ${on_string}"/>
		
	</outputs>

	<help>
	
Summary
-------
The kmer tool computes the distribution of footprints length from Bam file and determines the proportion of footprints beginning in each frame, for all annotated genes in the `GFF3`_ file.

		
.. _GFF3: http://gmod.org/wiki/GFF3
				
Output 
------- 
This tool provides an html report detailing the proportions and phasing of the kmers. 


Dependances
------------

.. class:: warningmark

This tool depends on Python (>=2.7) and following packages : numpy 1.8.0 and matplotlib 1.3.1. Samtools and pysam are used for bam manipulation.
		
	</help>
</tool>