view fastq_quality_boxplot.xml @ 3:cd82df766cab

Add missing help images.

<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.0">
	<description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
	<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>
<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 ([e-mail]) -->
</tool>