comparison blast/makeblastdb.xml @ 0:f3ac34855f5e default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

0:f3ac34855f5e

<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 &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>
    <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>