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/tools/metag_tools/short_reads_figure_score.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="quality_score_distribution" name="Build base quality distribution" version="1.0.2">
 2<description></description>
 3
 4<command interpreter="python">short_reads_figure_score.py $input1 $output1 </command>
 5
 6<inputs>
 7<page>
 8    <param name="input1" type="data" format="qualsolexa, qual454" label="Quality score file" help="No dataset? Read tip below"/>
 9</page>
10</inputs>
11
12<outputs>
13  	<data name="output1" format="png" />
14</outputs> 
15<requirements>
16	<requirement type="python-module">rpy</requirement>
17</requirements>
18<tests>
19	<test>
20		<param name="input1" value="solexa.qual" ftype="qualsolexa" />
21  		<output name="output1" file="solexaScore.png" ftype="png" />
22	</test>
23	<test>
24		<param name="input1" value="454.qual" ftype="qual454" />
25		<output name="output1" file="454Score.png" ftype="png" />
26	</test>
27</tests>
28<help>
29
30.. class:: warningmark
31
32To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples).
33
34-----
35
36**What it does**
37
38This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a graph showing score distribution like the one below. Such graph allows you to perform initial evaluation of data quality in a single pass.
39
40-----
41
42**Examples of Quality Data**
43
44Roche (454) or ABI SOLiD data::
45
46	&gt;seq1
47	23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
48
49Illumina (Solexa) data::
50
51 	-40 -40 40 -40	 -40 -40 -40 40	 
52 
53-----
54
55**Output example**
56
57Quality scores are summarized as boxplot (Roche 454 FLX data):
58
59.. image:: ${static_path}/images/short_reads_boxplot.png
60
61where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines:
62
63  - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths;
64  - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads.
65  
66Every box on the plot shows the following values::
67
68       o     &lt;---- Outliers
69       o
70      -+-    &lt;---- Upper Extreme Value that is no more 
71       |           than box length away from the box   
72       |
73    +--+--+  &lt;---- Upper Quartile
74    |     |
75    +-----+  &lt;---- Median
76    |     |
77    +--+--+  &lt;---- Lower Quartile 
78       |
79       |
80      -+-    &lt;---- Lower Extreme Value that is no more
81                   than box length away from the box
82       o     &lt;---- Outlier
83 
84 
85     
86</help>
87</tool>