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changeset 3:8d8552899d20

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Uploaded
author rlegendre
date Mon, 20 Oct 2014 11:07:03 -0400
parents da126b91f9ea
children eea5fec46e5c
files kmer_analysis.xml
diffstat 1 files changed, 43 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmer_analysis.xml	Mon Oct 20 11:07:03 2014 -0400
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+<tool id="kmer_analysis" name="Kmer">
+	<description>Compute proportion of each kmer and phasing</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="References Input 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"/>
+		
+	</outputs>
+
+	<help>
+	
+Summary
+-------
+This tool uses Ribo-seq data (bam file) to compute proportion of each kmer (lenght of footprints) and phasing. 
+		
+Output 
+------- 
+This tool provides an html report with all kmer proportion and phasing. 
+
+
+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>
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