--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_nucleotides_distribution.xml	Wed Sep 25 11:14:24 2013 -0400
@@ -0,0 +1,53 @@
+<tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart">
+	<description></description>
+    <requirements>
+        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
+    </requirements>
+	<command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
+	
+	<inputs>
+		<param format="txt" version="1.0.0" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
+	</inputs>
+	
+	<outputs>
+		<data format="png" version="1.0.0" name="output" metadata_source="input" />
+	</outputs>
+<help>
+
+**What it does**
+
+Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
+
+.. class:: infomark
+
+**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
+
+-----
+
+**Output Examples**
+
+The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
+
+.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png
+ 
+In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
+
+.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png
+
+The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
+
+.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png
+
+But most of the time, the chart will look rather random:
+
+.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+
+</help>
+<!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 11:14:24 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fastx_toolkit" version="0.0.13">
+        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>