view tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 20:3034ce97dd33 draft

Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.

<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@">
    <description>Show BLAST database information from blastdbcmd</description>
    <macros>
        <token name="@BINARY@">blastdbcmd</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble" />
    <command>
blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info"
    </command>
    <inputs>
        <expand macro="input_conditional_choose_db_type" />
    </inputs>
    <outputs>
        <data name="info" format="txt" label="${db_opts.database.fields.name} info" />
    </outputs>
    <tests>
        <test>
            <param name="db_opts|db_type" value="prot" />
            <param name="db_opts|database" value="four_human_proteins" />
            <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" />
        </test>
        <test>
            <param name="db_opts|db_type" value="nucl" />
            <param name="db_opts|database" value="three_human_mRNA" />
            <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" />
        </test>
        <test>
            <param name="db_opts|db_type" value="nucl" />
            <param name="db_opts|database" value="rhodopsin_nucs" />
            <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" lines_diff="4" />
        </test>
    </tests>
    <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:

@REFERENCES@
    </help>
    <expand macro="blast_citations" />
</tool>