Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 5:393a7a35383c draft
Uploaded v0.0.14 adding local BLAST database support.
This *requires* the matching update to the blast_datatypes repository. This adds basic wrappers for makeblastdb and blastdbinfo.
This update includes work by Edward Kirton.
author | peterjc |
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date | Fri, 09 Nov 2012 06:53:55 -0500 |
parents | |
children | 9dabbfd73c8a |
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4:9d5beacae92b | 5:393a7a35383c |
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.2"> | |
2 <description>Show BLAST database information from blastdbcmd</description> | |
3 <command> | |
4 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out $info | |
5 </command> | |
6 <stdio> | |
7 <!-- Anything other than zero is an error --> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 <!-- Suspect blastdbcmd sometimes fails to set error level --> | |
11 <regex match="Error:" /> | |
12 <regex match="EXception:" /> | |
13 </stdio> | |
14 <inputs> | |
15 <conditional name="db_opts"> | |
16 <param name="db_type" type="select" label="Type of BLAST database"> | |
17 <option value="nucl" selected="True">Nucleotide</option> | |
18 <option value="prot">Protein</option> | |
19 </param> | |
20 <when value="nucl"> | |
21 <param name="database" type="select" label="Nucleotide BLAST database"> | |
22 <options from_file="blastdb.loc"> | |
23 <column name="value" index="0"/> | |
24 <column name="name" index="1"/> | |
25 <column name="path" index="2"/> | |
26 </options> | |
27 </param> | |
28 </when> | |
29 <when value="prot"> | |
30 <param name="database" type="select" label="Protein BLAST database"> | |
31 <options from_file="blastdb_p.loc"> | |
32 <column name="value" index="0"/> | |
33 <column name="name" index="1"/> | |
34 <column name="path" index="2"/> | |
35 </options> | |
36 </param> | |
37 </when> | |
38 </conditional> | |
39 </inputs> | |
40 <outputs> | |
41 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | |
42 </outputs> | |
43 <requirements> | |
44 <requirement type="binary">blastdbcmd</requirement> | |
45 </requirements> | |
46 <help> | |
47 | |
48 **What it does** | |
49 | |
50 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
51 switch to give summary information about a BLAST database, such as | |
52 the size (number of sequences and total length) and date. | |
53 | |
54 ------- | |
55 | |
56 **References** | |
57 | |
58 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. | |
59 | |
60 Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. | |
61 | |
62 </help> | |
63 </tool> |