|
0
|
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
|
|
1
|
36 .. image:: fastq_quality_boxplot_1.png
|
|
0
|
37
|
|
|
38
|
|
|
39 A relatively good quality library (median quality degrades towards later cycles):
|
|
|
40
|
|
1
|
41 .. image:: fastq_quality_boxplot_2.png
|
|
0
|
42
|
|
|
43 A low quality library (median drops quickly):
|
|
|
44
|
|
1
|
45 .. image:: fastq_quality_boxplot_3.png
|
|
0
|
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) -->
|
|
1
|
57 </tool>
|
