comparison tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.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.

8:1f546099212f

<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.3">
    <description>Extract sequence(s) from BLAST database</description>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"

        <!-- 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>

        </param>
    </inputs>
    <outputs>
        <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
    </outputs>
    <requirements>
        <requirement type="binary">blastdbcmd</requirement>
    </requirements>
    <help>
    
**What it does**

Extracts FASTA formatted sequences from a BLAST database

9:9dabbfd73c8a

<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5">
    <description>Extract sequence(s) from BLAST database</description>
    <requirements>
        <requirement type="binary">blastdbcmd</requirement>
        <requirement type="package" version="2.2.26+">blast+</requirement>
    </requirements>
    <version_command>blastdbcmd -version</version_command>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"

        <!-- 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>

        </param>
    </inputs>
    <outputs>
        <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
    </outputs>
    <help>
    
**What it does**

Extracts FASTA formatted sequences from a BLAST database