Mercurial > repos > devteam > ncbi_blast_plus
view 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 |
---|---|
date | Thu, 25 Apr 2013 09:38:37 -0400 |
parents | 393a7a35383c |
children | 70e7dcbf6573 |
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<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> <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** Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. 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. </help> </tool>