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/tools/solid_tools/solid_qual_boxplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 40 lines | 25 code | 15 blank | 0 comment | 0 complexity | ed95adea556e5cce6a1eb41f5712d43f MD5 | raw file
 1<tool id="solid_qual_boxplot" name="Draw quality score boxplot" version="1.0.0">
 2	<description>for SOLiD data</description>
 3	
 4	<command interpreter="bash">qualsolid_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 'Quality Statistics for SOLiD data' 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
17Creates a boxplot graph for the quality scores in the library.
18
19.. class:: infomark
20
21**TIP:** Use the **Quality Statistics for SOLiD data** tool to generate the report file needed for this tool.
22
23-----
24
25**Output Example**
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 outliers at max. 1.5*IQR
30
31
32.. image:: ${static_path}/images/solid_qual.png
33
34------
35
36This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
37
38 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
39</help>
40</tool>