root/galaxy-central/tools/metag_tools/convert_SOLiD_color2nuc.xml @ 2

リビジョン 2, 1.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="color2nuc" name="Convert Color Space" version="1.0.0">
2<description> to Nucleotides </description>
3<command interpreter="python">convert_SOLiD_color2nuc.py $input1 $input2 $output1 </command>
4
5<inputs>
6    <param name="input1" type="data" format="txt" label="SOLiD color coding file" />
7    <param name="input2" type="select" label="Keep prefix nucleotide">
8        <option value="yes">Yes</option>
9        <option value="no">No</option>
10    </param>
11</inputs>
12<outputs>
13        <data name="output1" format="fasta" />
14</outputs>
15<!--
16<tests>
17        <test>
18                <param name="input1" value="convert_SOLiD_color2nuc_test1.txt" ftype="txt" />
19                <param name="input2" value="no" />
20                <output name="output1" file="convert_SOLiD_color2nuc_test1.out" />
21        </test>
22</tests>
23-->
24<help>
25
26.. class:: warningmark
27
28The tool was designed for color space files generated from an ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" character, and each color space sequence starts with a leading nucleotide.
29 
30-----
31
32**What it does**
33
34This tool converts a color space sequence to nucleotides. The leading character must be a nucleotide: A, C, G, or T.
35 
36-----
37
38**Example**
39
40- If the color space file looks like this::
41
42        &gt;seq1
43        A013
44        &gt;seq2
45        T011213122200221123032111221021210131332222101
46       
47- If you would like to **keep** the leading nucleotide::
48
49        &gt;seq1
50        AACG
51        &gt;seq2
52        TTGTCATGAGAAAGACAGCCGACACTCAAGTCAACGTATCTCTGGT
53       
54- If you **do not want to keep** the leading nucleotide (the length of nucleotide sequence will be one less than the color-space sequence)::
55 
56        &gt;seq1
57        ACG
58        &gt;seq2
59        TGTCATGAGAAAGACAGCCGACACTCAAGTCAACGTATCTCTGGT
60
61-----
62
63**ABI SOLiD Color Coding Alignment matrix**
64
65 Each di-nucleotide is represented by a single digit: 0 to 3. The matrix is symmetric, thus the leading nucleotide is necessary to determine the sequence (otherwise there are four possibilities).
66
67 
68 .. image:: ../static/images/dualcolorcode.png
69
70
71</help>
72</tool>
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