--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/ReadLengthDistributionMatrix.xml	Tue Jun 19 22:15:09 2012 -0400
@@ -0,0 +1,63 @@
+<tool id="ReadLengthDistributionMatrix" name="Create read length distribution matrix" version="1.0.0">
+  <description>across a genomic interval</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.ReadLengthDistributionMatrix -i $input --chr $chr --start $start --stop $stop --min $min --max $max --bin $bin -o $output</command>
+  <inputs>
+      <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
+      <param name="chr" type="text" label="Chromosome" />
+      <param name="start" type="integer" value="1" label="Start base pair" />
+      <param name="stop" type="integer" value="1000" label="Stop base pair" />
+      <param name="min" type="integer" value="1" label="Minimum fragment length (bp)" />
+      <param name="max" type="integer" value="200" label="Maximum fragment length (bp)" />
+      <param name="bin" type="integer" value="1" label="Fragment length bin size (bp)" />
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will create a matrix (in matrix2png_ format) with the distribution of read lengths over each base pair. Reads are binned by genomic location and length to create a matrix where each column represents the distribution of read lengths over that base pair. The resulting matrix can be turned into heatmap using the Visualization -> Make heatmap with matrix2png tool.
+  
+.. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
+  
+.. class:: warningmark
+
+This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.
+
+-----
+
+**Syntax**
+
+- **Mapped reads** are the mapped paired-end reads used to make the histograms
+- **Chromosome** a locus in the genome
+- **Start base pair** a locus in the genome
+- **Stop base pair** a locus in the genome
+- **Minimum fragment length** is the lowest fragment length bin. Reads shorter than this will be ignored.
+- **Maximum fragment length** is the highest fragment length bin. Reads longer than this will be ignored.
+- **Fragment length bin size** is the bin size used when making the fragment length histograms
+
+-----
+  
+**Example**
+
+Make a matrix with the read length distribution across the region chrI:5001-6000, looking at reads 100-200bp in length in bins of 1bp:
+
+- **Chromosome:** chrI
+- **Start:** 5001
+- **Stop:** 6000
+- **Minimum fragment length:** 100
+- **Maximum fragment length:** 200
+- **Fragment length bin size:** 1
+
+The resulting matrix will be 1000x101, with each column representing a base pair and each row representing a read length. The column headers give the base pair and the row headers give the read length.
+
+-----
+
+**Citation**
+
+This tool was inspired by the analysis and figures in 
+
+Floer M, Wang X, Prabhu V, Berrozpe G, Narayan S, Spagna D, Alvarez D, Kendall J, Krasnitz A, Stepansky A, Hicks J, Bryant GO and Ptashne M (2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell 141: 407–418
+
+</help>
+</tool>