fastq_quality_boxplot.xml

<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="@VERSION@">
    <description></description>
    <expand macro="requirements" />
    <macros>
        <import>fastx_macros.xml</import>
    </macros>
    <command>
        fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output'
    </command>
    <inputs>
        <param format="txt" name="input" type="data" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
    </inputs>

    <outputs>
        <data format="png" name="output" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fastq_stats1.out" ftype="txt"></param>
            <output name="output" file="quality_boxplot_out.png"></output>
        </test>
    </tests>
<help>

**What it does**

Creates a boxplot graph for the quality scores in the library.

.. class:: infomark

**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.

-----

**Output Examples**

* Black horizontal lines are medians
* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
* Whiskers show outlier at max. 1.5*IQR


An excellent quality library (median quality is 40 for almost all 36 cycles):

.. image:: fastq_quality_boxplot_1.png


A relatively good quality library (median quality degrades towards later cycles):

.. image:: fastq_quality_boxplot_2.png

A low quality library (median drops quickly):

.. image:: fastq_quality_boxplot_3.png

------

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

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



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