annotate 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.

<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.

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**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>