annotate tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 10:70e7dcbf6573 draft

Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.

<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5">
    <description>Make BLAST database</description>
    <requirements>
        <requirement type="binary">makeblastdb</requirement>
        <requirement type="package" version="2.2.26+">blast+</requirement>
    </requirements>
    <version_command>makeblastdb -version</version_command>
    <command>
makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
$parse_seqids
$hash_index
## Single call to -in with multiple filenames space separated with outer quotes
## (presumably any filenames with spaces would be a problem). Note this gives
## some extra spaces, e.g. -in " file1 file2 file3  " but BLAST seems happy:
-in "
#for $i in $in
${i.file}
#end for
"
#if $title:
-title "$title"
#else:
##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
-title "BLAST Database"
#end if
-dbtype $dbtype 
## #set $sep = '-mask_data '
## #for $i in $mask_data
## $sep${i.file}
## #set $set = ', '
## #end for 
## #set $sep = '-gi_mask -gi_mask_name '
## #for $i in $gi_mask
## $sep${i.file}
## #set $set = ', '
## #end for 
## #if $tax.select == 'id':
## -taxid $tax.id
## #else if $tax.select == 'map':
## -taxid_map $tax.map
## #end if
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <inputs>
        <param name="dbtype" type="select" display="radio" label="Molecule type of input">
            <option value="prot">protein</option>
            <option value="nucl">nucleotide</option>
        </param>
        <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)
        <repeat name="in" title="BLAST or FASTA Database" min="1">
            <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" />
        </repeat>
        -->
        <repeat name="in" title="FASTA file" min="1">
            <param name="file" type="data" format="fasta" />
        </repeat>
        <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />
        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
        <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />

        <!-- SEQUENCE MASKING OPTIONS -->
        <!-- TODO
        <repeat name="mask_data" title="Provide one or more files containing masking data">
            <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />
        </repeat>
        <repeat name="gi_mask" title="Create GI indexed masking data">
            <param name="file" type="data" format="asnb" label="Masking data output file" />
        </repeat>
        -->

        <!-- TAXONOMY OPTIONS -->
        <!-- TODO
        <conditional name="tax">
            <param name="select" type="select" label="Taxonomy options">
                <option value="">Do not assign sequences to Taxonomy IDs</option>
                <option value="id">Assign all sequences to one Taxonomy ID</option>
                <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option>
            </param>
            <when value="">
            </when>
            <when value="id">
                <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer &gt;=0" />
            </when>
            <when value="map">
                <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />
            </when>
        </conditional>
        -->
    </inputs>
    <outputs>
        <!-- If we only accepted one FASTA file, we could use its human name here... -->
        <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}">
            <change_format>
                <when input="dbtype" value="nucl" format="blastdbn" />
                <when input="dbtype" value="prot" format="blastdbp" />
            </change_format>
        </data>
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

Make BLAST database from one or more FASTA files and/or BLAST databases.

This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the
replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite.

<!--
Applying masks to an existing BLAST database will not change the original database; a new database will be created.
For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases.
-->

**Documentation**

http://www.ncbi.nlm.nih.gov/books/NBK1763/

**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>