Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
author | peterjc |
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date | Thu, 25 Apr 2013 09:38:37 -0400 |
parents | 393a7a35383c |
children | 70e7dcbf6573 |
rev | line source |
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9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> |
5 | 2 <description>Show BLAST database information from blastdbcmd</description> |
9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
3 <requirements> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
4 <requirement type="binary">blastdbcmd</requirement> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
5 <requirement type="package" version="2.2.26+">blast+</requirement> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
6 </requirements> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
7 <version_command>blastdbcmd -version</version_command> |
5 | 8 <command> |
9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" |
5 | 10 </command> |
11 <stdio> | |
12 <!-- Anything other than zero is an error --> | |
13 <exit_code range="1:" /> | |
14 <exit_code range=":-1" /> | |
15 <!-- Suspect blastdbcmd sometimes fails to set error level --> | |
16 <regex match="Error:" /> | |
9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
|
17 <regex match="Exception:" /> |
5 | 18 </stdio> |
19 <inputs> | |
20 <conditional name="db_opts"> | |
21 <param name="db_type" type="select" label="Type of BLAST database"> | |
22 <option value="nucl" selected="True">Nucleotide</option> | |
23 <option value="prot">Protein</option> | |
24 </param> | |
25 <when value="nucl"> | |
26 <param name="database" type="select" label="Nucleotide BLAST database"> | |
27 <options from_file="blastdb.loc"> | |
28 <column name="value" index="0"/> | |
29 <column name="name" index="1"/> | |
30 <column name="path" index="2"/> | |
31 </options> | |
32 </param> | |
33 </when> | |
34 <when value="prot"> | |
35 <param name="database" type="select" label="Protein BLAST database"> | |
36 <options from_file="blastdb_p.loc"> | |
37 <column name="value" index="0"/> | |
38 <column name="name" index="1"/> | |
39 <column name="path" index="2"/> | |
40 </options> | |
41 </param> | |
42 </when> | |
43 </conditional> | |
44 </inputs> | |
45 <outputs> | |
46 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | |
47 </outputs> | |
48 <help> | |
49 | |
50 **What it does** | |
51 | |
52 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
53 switch to give summary information about a BLAST database, such as | |
54 the size (number of sequences and total length) and date. | |
55 | |
56 ------- | |
57 | |
58 **References** | |
59 | |
60 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. | |
61 | |
62 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. | |
63 | |
64 </help> | |
65 </tool> |