Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
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date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | 70e7dcbf6573 |
children | 623f727cdff1 |
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10:70e7dcbf6573 | 11:4c4a0da938ff |
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> | 1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.22"> |
2 <description>Show BLAST database information from blastdbcmd</description> | 2 <description>Show BLAST database information from blastdbcmd</description> |
3 <requirements> | 3 <macros> |
4 <requirement type="binary">blastdbcmd</requirement> | 4 <token name="@BINARY@">blastdbcmd</token> |
5 <requirement type="package" version="2.2.26+">blast+</requirement> | 5 <import>ncbi_macros.xml</import> |
6 </requirements> | 6 </macros> |
7 <version_command>blastdbcmd -version</version_command> | 7 <expand macro="requirements" /> |
8 <command> | 8 <command> |
9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" | 9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" |
10 </command> | 10 </command> |
11 <stdio> | 11 <expand macro="stdio" /> |
12 <!-- Anything other than zero is an error --> | |
13 <exit_code range="1:" /> | |
14 <exit_code range=":-1" /> | |
15 <!-- Suspect blastdbcmd sometimes fails to set error level --> | |
16 <regex match="Error:" /> | |
17 <regex match="Exception:" /> | |
18 </stdio> | |
19 <inputs> | 12 <inputs> |
20 <conditional name="db_opts"> | 13 <expand macro="input_conditional_choose_db_type" /> |
21 <param name="db_type" type="select" label="Type of BLAST database"> | |
22 <option value="nucl" selected="True">Nucleotide</option> | |
23 <option value="prot">Protein</option> | |
24 </param> | |
25 <when value="nucl"> | |
26 <param name="database" type="select" label="Nucleotide BLAST database"> | |
27 <options from_file="blastdb.loc"> | |
28 <column name="value" index="0"/> | |
29 <column name="name" index="1"/> | |
30 <column name="path" index="2"/> | |
31 </options> | |
32 </param> | |
33 </when> | |
34 <when value="prot"> | |
35 <param name="database" type="select" label="Protein BLAST database"> | |
36 <options from_file="blastdb_p.loc"> | |
37 <column name="value" index="0"/> | |
38 <column name="name" index="1"/> | |
39 <column name="path" index="2"/> | |
40 </options> | |
41 </param> | |
42 </when> | |
43 </conditional> | |
44 </inputs> | 14 </inputs> |
45 <outputs> | 15 <outputs> |
46 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | 16 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> |
47 </outputs> | 17 </outputs> |
48 <help> | 18 <help> |
58 **References** | 28 **References** |
59 | 29 |
60 If you use this Galaxy tool in work leading to a scientific publication please | 30 If you use this Galaxy tool in work leading to a scientific publication please |
61 cite the following papers: | 31 cite the following papers: |
62 | 32 |
63 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | 33 @REFERENCES@ |
64 Galaxy tools and workflows for sequence analysis with applications | |
65 in molecular plant pathology. PeerJ 1:e167 | |
66 http://dx.doi.org/10.7717/peerj.167 | |
67 | |
68 Christiam Camacho et al. (2009). | |
69 BLAST+: architecture and applications. | |
70 BMC Bioinformatics. 15;10:421. | |
71 http://dx.doi.org/10.1186/1471-2105-10-421 | |
72 | |
73 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
74 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus | |
75 </help> | 34 </help> |
76 </tool> | 35 </tool> |