<tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
fastx_nucleotide_distribution_graph.sh
-t '$input.name'
-i '$input'
-o '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" />
    </inputs>
    <outputs>
        <data name="output" format="png" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fastx_nucleotides_distribution-in1.txt" />
            <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
        </test>
    </tests>
    <help><![CDATA[
**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:: 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:: 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:: fastq_nucleotides_distribution_3.png

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

.. image:: fastq_nucleotides_distribution_4.png

------

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

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    ]]></help>
    <expand macro="citations" />
    <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>