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comparison tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 9:9dabbfd73c8a draft

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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
date Thu, 25 Apr 2013 09:38:37 -0400
parents 393a7a35383c
children 70e7dcbf6573
comparison
equal deleted inserted replaced
8:1f546099212f 9:9dabbfd73c8a
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