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view ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 27:61f402b6e240 draft
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author | peterjc |
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date | Wed, 11 Sep 2013 06:26:20 -0400 |
parents | 688f3fb09a6a |
children | 4ae1bac976f3 |
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<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> <description>Show BLAST database information from blastdbcmd</description> <requirements> <requirement type="binary">blastdbcmd</requirement> <requirement type="package" version="2.2.26+">blast+</requirement> </requirements> <version_command>blastdbcmd -version</version_command> <command> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> <!-- Suspect blastdbcmd sometimes fails to set error level --> <regex match="Error:" /> <regex match="Exception:" /> </stdio> <inputs> <conditional name="db_opts"> <param name="db_type" type="select" label="Type of BLAST database"> <option value="nucl" selected="True">Nucleotide</option> <option value="prot">Protein</option> </param> <when value="nucl"> <param name="database" type="select" label="Nucleotide BLAST database"> <options from_file="blastdb.loc"> <column name="value" index="0"/> <column name="name" index="1"/> <column name="path" index="2"/> </options> </param> </when> <when value="prot"> <param name="database" type="select" label="Protein BLAST database"> <options from_file="blastdb_p.loc"> <column name="value" index="0"/> <column name="name" index="1"/> <column name="path" index="2"/> </options> </param> </when> </conditional> </inputs> <outputs> <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> </outputs> <help> **What it does** Calls the NCBI BLAST+ blastdbcmd command line tool with the -info switch to give summary information about a BLAST database, such as the size (number of sequences and total length) and date. ------- **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167 Christiam Camacho et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics. 15;10:421. http://dx.doi.org/10.1186/1471-2105-10-421 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>