Mercurial > repos > edward-kirton > blast
view blast/makeblastdb.xml @ 0:f3ac34855f5e default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:30:11 -0400 |
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<tool id="makeblastdb" name="makeblastdb" version="0.0.1"> <description>Make BLAST database</description> <command interpreter="bash">blastdb_wrapper.sh $outfile.extra_files_path makeblastdb -logfile $outfile -out ${os.path.join($outfile.extra_files_path,'blastdb')} -parse_seqids $hash_index #set $sep = '-in ' #for $i in $in $sep${i.file} #set $set = ', ' #end for -title $title -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 #elsif $tax.select == 'map': -taxid_map $tax.map #end if </command> <inputs> <repeat name="in" title="Blast or Fasta Database"> <param name="file" type="data" format="fasta,blastdb" label="Blast or Fasta database" /> </repeat> <param name="title" type="text" value="" label="Title for BLAST database" /> <param name="dbtype" type="select" display="radio" label="[-dbtype] Molecule type of input"> <option value="prot">protein</option> <option value="nucl">nucleotide</option> </param> <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="[-hash_index] Enables the creation of sequence hash values. These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> <!-- SEQUENCE MASKING OPTIONS --> <repeat name="mask_data" title="[-mask_data] 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="[-gi_mask_name] Create GI indexed masking data"> <param name="file" type="data" format="asnb" label="Masking data output file" /> </repeat> <!-- TAXONOMY OPTIONS --> <conditional name="tax"> <param name="select" type="select" label="Taxonomy options"> <option value="">Do not assign sequences to Taxonomy IDs</option> <option value="id">[-taxid] Assign all sequences to one Taxonomy ID</option> <option value="map">[-taxid_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> <data name="outfile" format="blastdb" /> </outputs> <requirements> </requirements> <help> **What it does** Make BLAST database from one or more FASTA files and/or BLAST databases. This application serves as a replacement for formatdb. 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/ </help> </tool>