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/tools/metag_tools/short_reads_figure_high_quality_length.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 75 lines | 51 code | 24 blank | 0 comment | 0 complexity | d49253b2321a3a72089a25ccc3af9e9d MD5 | raw file
 1<tool id="hist_high_quality_score" name="Histogram">
 2<description> of high quality score reads </description>
 3
 4<command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command>
 5
 6<inputs>
 7<page>
 8    <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
 9    <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
10</page>
11</inputs>
12<outputs>
13  	<data name="output1" format="pdf" />
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		<param name="input2" value="5" />
22  		<output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
23	</test>
24	<test>
25		<param name="input1" value="454.qual" ftype="qual454" />
26		<param name="input2" value="5" />
27		<output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
28	</test>
29</tests>
30
31<help>
32
33.. class:: warningmark
34
35To 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).
36
37-----
38
39**What it does**
40
41This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a histogram of lengths of high quality reads.
42
43-----
44
45**Examples of Quality Data**
46
47Roche (454) or ABI SOLiD data::
48
49	&gt;seq1
50	23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
51
52Illumina (Solexa) data::
53
54 	-40 -40 40 -40	 -40 -40 -40 40	 
55 
56-----
57
58**Note**
59
60- Quality score data::
61
62	&gt;seq1
63	23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
64
65- If the threshold is set to 20:
66
67  - a low quality score 4 in the middle separated two segments of lengths 11 and 5.
68
69  - The histogram will be built based on the numbers (11, 5).
70	 	
71- For Illumina (Solexa) data, only the maximal of the 4 values will be used.
72
73
74</help>
75</tool>