Mercurial > repos > devteam > megablast_wrapper
annotate megablast_wrapper.xml @ 1:fb2e0e1dac89 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_wrapper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:20:16 -0500 |
parents | dc7b4acb3fa6 |
children |
rev | line source |
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0 | 1 <tool id="megablast_wrapper" name="Megablast" version="1.2.0"> |
2 <description> compare short reads against htgs, nt, and wgs databases</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.2.26+">blast+</requirement> | |
5 <requirement type="package" version="0.7.1">bx-python</requirement> | |
6 </requirements> | |
7 <command interpreter="python"> | |
8 megablast_wrapper.py | |
9 --db_build="${source_select.fields.path}" | |
10 --input=$input_query | |
11 --word_size=$word_size | |
12 --identity_cutoff=$iden_cutoff | |
13 --eval_cutoff=$evalue_cutoff | |
14 --filter_query=$filter_query | |
15 --index_dir=${GALAXY_DATA_INDEX_DIR} | |
16 --output=$output1 | |
17 </command> | |
18 <inputs> | |
19 <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> | |
20 <param name="source_select" type="select" display="radio" label="against target database"> | |
21 <options from_data_table="blastdb" /> | |
22 </param> | |
23 <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-word_size)"> | |
24 <option value="28">28</option> | |
25 <option value="16">16</option> | |
26 </param> | |
1
fb2e0e1dac89
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_wrapper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
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27 <param name="iden_cutoff" type="float" value="90.0" label="report hits above this identity (-perc_identity)" help="no cutoff if 0" /> |
fb2e0e1dac89
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_wrapper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
28 <param name="evalue_cutoff" type="float" value="0.001" label="set expectation value cutoff (-evalue)" /> |
0 | 29 <param name="filter_query" type="select" label="Filter out low complexity regions? (-dust)"> |
30 <option value="yes">Yes</option> | |
31 <option value="no">No</option> | |
32 </param> | |
33 </inputs> | |
34 <outputs> | |
35 <data name="output1" format="tabular"/> | |
36 </outputs> | |
37 <tests> | |
38 <test> | |
39 <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> | |
40 <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> | |
41 <param name="source_select" value="phiX" /> | |
42 <param name="word_size" value="28" /> | |
43 <param name="iden_cutoff" value="99.0" /> | |
44 <param name="evalue_cutoff" value="10.0" /> | |
45 <param name="filter_query" value="yes" /> | |
46 <output name="output1" file="megablast_wrapper_test1.out"/> | |
47 </test> | |
48 </tests> | |
49 <help> | |
50 | |
51 .. class:: warningmark | |
52 | |
53 **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. | |
54 | |
55 ----- | |
56 | |
57 **What it does** | |
58 | |
59 This tool runs **megablast** function of BLAST+ blastn tool - a high performance nucleotide local aligner developed by Webb Miller and colleagues. | |
60 | |
61 ----- | |
62 | |
63 **Output format** | |
64 | |
65 Output of this tool contains 13 columns delimited by Tabs: | |
66 | |
67 1. Id of your sequence | |
68 2. GI of the database hit | |
69 3. Length of the database hit | |
70 4. % identity | |
71 5. Alignment length | |
72 6. # mismatches | |
73 7. # gaps | |
74 8. Start position in your sequence | |
75 9. End position in your sequence | |
76 10. Start position in database hit | |
77 11. End position in database hit | |
78 12. E-value | |
79 13. Bit score | |
80 | |
81 ------- | |
82 | |
83 **Reference** | |
84 | |
85 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. | |
86 | |
87 </help> | |
88 </tool> |