comparison tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml @ 11:4c4a0da938ff draft

Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.

10:70e7dcbf6573

<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6">
    <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}"

| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq"
#else:
| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
#end if
    </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>
        <conditional name="id_opts">
            <param name="id_type" type="select" label="Type of identifier list">
              <option value="file">From file</option>
              <option value="prompt">User entered</option>
            </param>

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

Christiam Camacho et al. (2009).
BLAST+: architecture and applications.
BMC Bioinformatics. 15;10:421.
http://dx.doi.org/10.1186/1471-2105-10-421

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
    </help>
</tool>

11:4c4a0da938ff

<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.22">
    <description>Extract sequence(s) from BLAST database</description>
    <macros>
        <token name="@BINARY@">blastdbcmd</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <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}"

| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq"
#else:
| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
#end if
    </command>
    <expand macro="stdio" />
    <inputs>
        <expand macro="input_conditional_choose_db_type" />
        <conditional name="id_opts">
            <param name="id_type" type="select" label="Type of identifier list">
              <option value="file">From file</option>
              <option value="prompt">User entered</option>
            </param>

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

@REFERENCES@
    </help>
</tool>