root/galaxy-central/tools/metag_tools/blat_wrapper.xml

リビジョン 2, 3.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="blat_wrapper" name="BLAT" version="1.0.0">
2  <description> compare sequencing reads against UCSC genome builds</description>
3  <command interpreter="python">
4    #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
5    #else                                 #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
6    #end if# ${GALAXY_DATA_INDEX_DIR}
7  </command>
8        <inputs>
9        <conditional name="source">
10                <param name="source_select" type="select" label="Target source">
11                                <option value="database">Genome Build</option>
12                                <option value="input_ref">Your Upload File</option>
13                </param>
14                <when value="database">
15                        <param name="dbkey" type="genomebuild" label="Genome" />
16                </when>
17                <when value="input_ref">
18                        <param name="input_target" type="data" format="fasta" label="Reference sequence" />
19                </when>
20        </conditional> 
21                <param name="input_query" type="data" format="fasta" label="Sequence file"/>
22                <param name="iden" type="float" size="15" value="90.0" label="Minimal identity (-minIdentity)" />
23                <param name="tile_size" type="integer" size="15" value="11" label="Minimal size of exact match (-tileSize)" help="Must be between 6 and 18."/>
24                <param name="one_off" type="integer" size="15" value="0" label="Number of mismatch in the word (-oneOff)" help="Must be between 0 and 2." />
25        </inputs>
26        <outputs>
27                <data name="output1" format="tabular"/>
28        </outputs>
29        <requirements>
30          <requirement type="binary">blat</requirement>
31        </requirements>
32        <tests>
33                <test>
34                <param name="source_select" value="database" />
35                <param name="dbkey" value="eschColi_K12" />
36                <param name="input_query" value="blat_wrapper_test1.fa" ftype="fasta"/>
37                <param name="iden" value="90.0" />
38                <param name="tile_size" value="11" />
39                <param name="one_off" value="0" />
40                <output name="output1" file="blat_wrapper_test1.out" />
41                </test>
42        </tests>
43        <help>
44       
45.. class:: warningmark
46
47Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time.
48
49.. class:: warningmark
50
51Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time.
52
53-----
54       
55**What it does**
56 
57This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file.
58 
59-----
60 
61**Example**
62 
63- Input a multiple fasta file::
64
65        &gt;seq1
66        TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT
67
68- Use the default settings:
69
70  - alignment identity must be higher than or equal to 90%.
71 
72  - minimal size of exact match to trigger an alignment is 11.
73 
74  - allow 0 mismatches in the above exact match size.
75 
76- Search against ce2 (C. elegans March 2004), partial result::
77
78        25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt,
79        27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt,
80
81-----
82
83**Parameters**
84
85- *Minimal Identity* (**-minIdentity**) : In percent, the minimum sequence identity between the query and target alignment. Default is 90.
86
87- *Minimal Size of Exact Match* (**-tileSize**) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18.
88
89- *Number of Mismatch in the Word* (**-oneOff**) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0.
90
91-----
92
93**Reference**
94 
95 **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.
96
97
98        </help>
99</tool>
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