Mercurial > repos > devteam > short_reads_figure_high_quality_length
comparison short_reads_figure_high_quality_length.xml @ 0:556ceed24699 draft
Imported from capsule None
author | devteam |
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date | Mon, 19 May 2014 12:34:37 -0400 |
parents | |
children | 76c4a4ed8e74 |
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1 <tool id="hist_high_quality_score" name="Histogram" version="1.0.0"> | |
2 <description> of high quality score reads </description> | |
3 <requirements> | |
4 <requirement type="package" version="1.0.3">rpy</requirement> | |
5 <requirement type="package" version="2.11.0">R</requirement> | |
6 </requirements> | |
7 <command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command> | |
8 <inputs> | |
9 <page> | |
10 <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> | |
11 <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" /> | |
12 </page> | |
13 </inputs> | |
14 <outputs> | |
15 <data name="output1" format="pdf" /> | |
16 </outputs> | |
17 <tests> | |
18 <test> | |
19 <param name="input1" value="solexa.qual" ftype="qualsolexa" /> | |
20 <param name="input2" value="5" /> | |
21 <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/> | |
22 </test> | |
23 <test> | |
24 <param name="input1" value="454.qual" ftype="qual454" /> | |
25 <param name="input2" value="5" /> | |
26 <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/> | |
27 </test> | |
28 </tests> | |
29 | |
30 <help> | |
31 | |
32 .. class:: warningmark | |
33 | |
34 To 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). | |
35 | |
36 ----- | |
37 | |
38 **What it does** | |
39 | |
40 This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a histogram of lengths of high quality reads. | |
41 | |
42 ----- | |
43 | |
44 **Examples of Quality Data** | |
45 | |
46 Roche (454) or ABI SOLiD data:: | |
47 | |
48 >seq1 | |
49 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
50 | |
51 Illumina (Solexa) data:: | |
52 | |
53 -40 -40 40 -40 -40 -40 -40 40 | |
54 | |
55 ----- | |
56 | |
57 **Note** | |
58 | |
59 - Quality score data:: | |
60 | |
61 >seq1 | |
62 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
63 | |
64 - If the threshold is set to 20: | |
65 | |
66 - a low quality score 4 in the middle separated two segments of lengths 11 and 5. | |
67 | |
68 - The histogram will be built based on the numbers (11, 5). | |
69 | |
70 - For Illumina (Solexa) data, only the maximal of the 4 values will be used. | |
71 | |
72 | |
73 </help> | |
74 </tool> |