<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
#import re
#set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
fastq_quality_boxplot_graph.sh
-t '$escaped_element_identifier'
-i '$input'
-o '$output'
    ]]></command>

    <inputs>
        <param name="input" type="data" format="txt" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
    </inputs>

    <outputs>
        <data name="output" format="png" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fastq_quality_boxplot-in1.fastq" />
            <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="10000" />
        </test>
    </tests>
    <help><![CDATA[
**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>
    <expand macro="citations" />
<!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>