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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastq_quality_boxplot.xml @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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2:dfe9332138cf 3:997f5136985f
1 <tool id="cshl_fastq_quality_boxplot" name="Quality Score">
2 <description>chart</description>
3
4 <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
5
6 <inputs>
7 <param format="txt" name="input" type="data" label="Statistics report file (output of 'FASTQ Statistics' tool)" />
8 </inputs>
9
10 <outputs>
11 <data format="png" name="output" metadata_source="input" />
12 </outputs>
13 <help>
14
15 **What it does**
16
17 Creates a boxplot graph for the quality scores in the library.
18
19 .. class:: infomark
20
21 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
22
23 -----
24
25 **Output Examples**
26
27 * Black horizontal lines are medians
28 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
29 * Whiskers show outlier at max. 1.5*IQR
30
31
32 An excellent quality library (median quality is 40 for almost all 36 cycles):
33
34 .. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png
35
36
37 A relatively good quality library (median quality degrades towards later cycles):
38
39 .. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
40
41 A low quality library (median drops quickly):
42
43 .. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
44
45 </help>
46 </tool>
47 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->