Mercurial > repos > xuebing > sharplabtool
comparison tools/metag_tools/megablast_wrapper.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="megablast_wrapper" name="Megablast" version="1.1.0"> | |
2 <description> compare short reads against htgs, nt, and wgs databases</description> | |
3 <command interpreter="python"> | |
4 megablast_wrapper.py | |
5 --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" | |
6 --input=$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_data_table="blastdb" /> | |
18 </param> | |
19 <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)"> | |
20 <option value="28">28</option> | |
21 <option value="16">16</option> | |
22 </param> | |
23 <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" /> | |
24 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" /> | |
25 <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)"> | |
26 <option value="T">Yes</option> | |
27 <option value="F">No</option> | |
28 </param> | |
29 </inputs> | |
30 <outputs> | |
31 <data name="output1" format="tabular"/> | |
32 </outputs> | |
33 <requirements> | |
34 <requirement type="package">megablast</requirement> | |
35 </requirements> | |
36 <tests> | |
37 <test> | |
38 <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> | |
39 <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> | |
40 <param name="source_select" value="/galaxy/data/blastdb/phiX/phiX" /> | |
41 <param name="word_size" value="28" /> | |
42 <param name="iden_cutoff" value="99.0" /> | |
43 <param name="evalue_cutoff" value="10.0" /> | |
44 <param name="filter_query" value="T" /> | |
45 <output name="output1" file="megablast_wrapper_test1.out"/> | |
46 </test> | |
47 </tests> | |
48 <help> | |
49 | |
50 .. class:: warningmark | |
51 | |
52 **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. | |
53 | |
54 ----- | |
55 | |
56 **What it does** | |
57 | |
58 This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues. | |
59 | |
60 ----- | |
61 | |
62 **Output format** | |
63 | |
64 Output of this tool contains 13 columns delimited by Tabs: | |
65 | |
66 1. Id of your sequence | |
67 2. GI of the database hit | |
68 3. Length of the database hit | |
69 4. % identity | |
70 5. Alignment length | |
71 6. # mismatches | |
72 7. # gaps | |
73 8. Start position in your sequence | |
74 9. End position in your sequence | |
75 10. Start position in database hit | |
76 11. End position in database hit | |
77 12. E-value | |
78 13. Bit score | |
79 | |
80 ------- | |
81 | |
82 **Reference** | |
83 | |
84 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. | |
85 | |
86 </help> | |
87 </tool> |