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

リビジョン 2, 3.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="megablast_wrapper" name="Megablast" version="1.0.5">
2    <description> compare short reads against htgs, nt, and wgs databases</description>
3    <command interpreter="python">
4      megablast_wrapper.py
5       --db_build="$source_select"
6       --input=$input_query
7       --word_size=$word_size
8       --identity_cutoff=$iden_cutoff
9       --eval_cutoff=$evalue_cutoff
10       --filter_query=$filter_query
11       --index_dir=${GALAXY_DATA_INDEX_DIR}
12       --output=$output1
13    </command>
14    <inputs>
15        <param name="input_query" type="data" format="fasta" label="Compare these sequences"/>
16        <param name="source_select" type="select" display="radio" label="against target database">
17            <options from_file="blastdb.loc">
18              <column name="name" index="0"/>
19              <column name="value" index="0"/>
20            </options>
21        </param>
22        <param name="word_size" type="select" label="using word size" help="Size of best perfect match">
23            <option value="28">28</option>
24            <option value="16">16</option>
25        </param>
26        <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" />
27        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
28        <param name="filter_query" type="select" label="Filter out low complexity regions?">
29            <option value="T">Yes</option>
30            <option value="F">No</option>
31        </param>
32    </inputs>
33    <outputs>
34        <data name="output1" format="tabular"/>
35    </outputs>
36    <requirements>
37        <requirement type="package">megablast</requirement>
38    </requirements>
39    <tests>
40        <test>
41            <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
42            <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate -->
43            <param name="source_select" value="phiX" />
44            <param name="word_size" value="28" />
45            <param name="iden_cutoff" value="99.0" />
46            <param name="evalue_cutoff" value="10.0" />
47            <param name="filter_query" value="T" />
48            <output name="output1" file="megablast_wrapper_test1.out"/>
49        </test>
50    </tests>
51    <help>
52   
53.. class:: warningmark
54
55**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. 
56
57-----
58
59**What it does**
60
61This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues.
62
63-----
64
65**Output format**
66
67Output of this tool contains 13 columns delimited by Tabs:
68
691. Id of your sequence
702. GI of the database hit
713. Length of the database hit
724. % identity
735. Alignment length
746. # mismatches
757. # gaps
768. Start position in your sequence
779. End position in your sequence
7810. Start position in database hit
7911. End position in database hit
8012. E-value
8113. Bit score
82
83-------
84
85**Reference**
86
87Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
88
89    </help>
90</tool>
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