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/tools/fastx_toolkit/fastq_quality_boxplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
 2	<description></description>
 3	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 4	
 5	<command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
 6	
 7	<inputs>
 8		<param format="txt" name="input" type="data" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
 9	</inputs>
10
11	<outputs>
12		<data format="png" name="output" metadata_source="input" />
13	</outputs>
14<help>
15
16**What it does**
17
18Creates a boxplot graph for the quality scores in the library.
19
20.. class:: infomark
21
22**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
23
24-----
25
26**Output Examples**
27
28* Black horizontal lines are medians
29* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
30* Whiskers show outlier at max. 1.5*IQR
31
32
33An excellent quality library (median quality is 40 for almost all 36 cycles):
34
35.. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png
36
37
38A relatively good quality library (median quality degrades towards later cycles):
39
40.. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
41
42A low quality library (median drops quickly):
43
44.. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
45
46------
47
48This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
49
50 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
51
52
53
54</help>
55</tool>
56<!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->