view tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 27:6f8ea4b9a2c4 draft

"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"

<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Show BLAST database information from blastdbcmd</description>
    <macros>
        <token name="@BINARY@">blastdbcmd</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble" />
    <command detect_errors="aggressive">
blastdbcmd
@DBCMD_OPTS@
-info -out "$info"
    </command>
    <inputs>
        <expand macro="input_conditional_choose_db_type" />
    </inputs>
    <outputs>
        <data name="info" format="txt" label="@ON_DBCMD_OPTS@ info" />
    </outputs>
    <tests>
        <test>
            <param name="db_opts|db_type" value="prot" />
            <param name="db_opts|db_origin|database" value="four_human_proteins" />
            <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" compare="contains" />
        </test>
        <test>
            <param name="db_opts|db_type" value="nucl" />
            <param name="db_opts|db_origin|database" value="three_human_mRNA" />
            <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" compare="contains" />
        </test>
        <test>
            <param name="db_opts|db_type" value="nucl" />
            <param name="db_opts|db_origin|database" value="rhodopsin_nucs" />
            <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" />
        </test>
        <test>
            <param name="db_opts|db_type" value="nucl" />
            <param name="db_opts|db_origin|database" value="three_human_mRNA,rhodopsin_nucs" />
            <output name="info" file="three_human_mRNA_and_rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" />
        </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>