root/galaxy-central/tools/fastx_toolkit/fastx_nucleotides_distribution.xml

<tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
        <description></description>
        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
        <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
        
        <inputs>
                <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
        </inputs>
        
        <outputs>
                <data format="png" 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/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/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/fastx_icons/fastq_nucleotides_distribution_3.png

But most of the time, the chart will look rather random:

.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/

</help>
</tool>
<!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->