Mercurial > repos > devteam > ncbi_blast_plus
comparison 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 |
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8:1f546099212f | 9:9dabbfd73c8a |
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.2"> | 1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> |
2 <description>Show BLAST database information from blastdbcmd</description> | 2 <description>Show BLAST database information from blastdbcmd</description> |
3 <requirements> | |
4 <requirement type="binary">blastdbcmd</requirement> | |
5 <requirement type="package" version="2.2.26+">blast+</requirement> | |
6 </requirements> | |
7 <version_command>blastdbcmd -version</version_command> | |
3 <command> | 8 <command> |
4 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 "$info" |
5 </command> | 10 </command> |
6 <stdio> | 11 <stdio> |
7 <!-- Anything other than zero is an error --> | 12 <!-- Anything other than zero is an error --> |
8 <exit_code range="1:" /> | 13 <exit_code range="1:" /> |
9 <exit_code range=":-1" /> | 14 <exit_code range=":-1" /> |
10 <!-- Suspect blastdbcmd sometimes fails to set error level --> | 15 <!-- Suspect blastdbcmd sometimes fails to set error level --> |
11 <regex match="Error:" /> | 16 <regex match="Error:" /> |
12 <regex match="EXception:" /> | 17 <regex match="Exception:" /> |
13 </stdio> | 18 </stdio> |
14 <inputs> | 19 <inputs> |
15 <conditional name="db_opts"> | 20 <conditional name="db_opts"> |
16 <param name="db_type" type="select" label="Type of BLAST database"> | 21 <param name="db_type" type="select" label="Type of BLAST database"> |
17 <option value="nucl" selected="True">Nucleotide</option> | 22 <option value="nucl" selected="True">Nucleotide</option> |
38 </conditional> | 43 </conditional> |
39 </inputs> | 44 </inputs> |
40 <outputs> | 45 <outputs> |
41 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | 46 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> |
42 </outputs> | 47 </outputs> |
43 <requirements> | |
44 <requirement type="binary">blastdbcmd</requirement> | |
45 </requirements> | |
46 <help> | 48 <help> |
47 | 49 |
48 **What it does** | 50 **What it does** |
49 | 51 |
50 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | 52 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info |