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comparison tools/fastx_toolkit/fastq_quality_boxplot.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
18 Creates 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
33 An 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
38 A relatively good quality library (median quality degrades towards later cycles):
39
40 .. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
41
42 A low quality library (median drops quickly):
43
44 .. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
45
46 ------
47
48 This 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) -->