# HG changeset patch
# User rlegendre
# Date 1413817623 14400
# Node ID 8d8552899d20a9c4ba368cdb347afa7d8e5069ee
# Parent  da126b91f9ea2a6ff13861cc7f32928e4d309caa
Uploaded

diff -r da126b91f9ea -r 8d8552899d20 kmer_analysis.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmer_analysis.xml	Mon Oct 20 11:07:03 2014 -0400
@@ -0,0 +1,43 @@
+<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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