Mercurial > repos > xuebing > sharplabtool
comparison tools/metag_tools/short_reads_figure_high_quality_length.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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 | |
35 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). | |
36 | |
37 ----- | |
38 | |
39 **What it does** | |
40 | |
41 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. | |
42 | |
43 ----- | |
44 | |
45 **Examples of Quality Data** | |
46 | |
47 Roche (454) or ABI SOLiD data:: | |
48 | |
49 >seq1 | |
50 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
51 | |
52 Illumina (Solexa) data:: | |
53 | |
54 -40 -40 40 -40 -40 -40 -40 40 | |
55 | |
56 ----- | |
57 | |
58 **Note** | |
59 | |
60 - Quality score data:: | |
61 | |
62 >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> |