Mercurial > repos > devteam > ncbi_blast_plus
diff 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.
| author | peterjc |
|---|---|
| date | Mon, 23 Sep 2013 06:14:13 -0400 |
| parents | 9dabbfd73c8a |
| children | 4c4a0da938ff |
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--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,5 +1,5 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4"> - <description>Make BLAST database</description> +<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> @@ -14,7 +14,8 @@ ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy: -in " #for $i in $in -${i.file} #end for +${i.file} +#end for " #if $title: -title "$title" @@ -38,71 +39,73 @@ ## #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." /> + </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> - --> + <!-- 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 >=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 ${on_string}"> - <change_format> - <when input="dbtype" value="nucl" format="blastdbn"/> - <when input="dbtype" value="prot" format="blastdbp"/> - </change_format> - </data> -</outputs> -<help> + <!-- TAXONOMY OPTIONS --> + <!-- TODO + <conditional name="tax"> + <param name="select" type="select" label="Taxonomy options"> + <option value="">Do not assign sequences to Taxonomy IDs</option> + <option value="id">Assign all sequences to one Taxonomy ID</option> + <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> + </param> + <when value=""> + </when> + <when value="id"> + <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> + </when> + <when value="map"> + <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> + </when> + </conditional> + --> + </inputs> + <outputs> + <!-- If we only accepted one FASTA file, we could use its human name here... --> + <data name="outfile" format="data" label="${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. @@ -118,5 +121,23 @@ **Documentation** http://www.ncbi.nlm.nih.gov/books/NBK1763/ -</help> + +**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>