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comparison fastq_quality_boxplot.xml @ 0:e359ce20fbd9

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author devteam
date Wed, 25 Sep 2013 14:59:09 -0400
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1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
7
8 <inputs>
9 <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
10 </inputs>
11
12 <outputs>
13 <data format="png" name="output" metadata_source="input" />
14 </outputs>
15 <help>
16
17 **What it does**
18
19 Creates a boxplot graph for the quality scores in the library.
20
21 .. class:: infomark
22
23 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
24
25 -----
26
27 **Output Examples**
28
29 * Black horizontal lines are medians
30 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
31 * Whiskers show outlier at max. 1.5*IQR
32
33
34 An excellent quality library (median quality is 40 for almost all 36 cycles):
35
36 .. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_1.png
37
38
39 A relatively good quality library (median quality degrades towards later cycles):
40
41 .. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_2.png
42
43 A low quality library (median drops quickly):
44
45 .. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_3.png
46
47 ------
48
49 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
50
51 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
52
53
54
55 </help>
56 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
57 </tool>