diff tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 5:393a7a35383c draft

Uploaded v0.0.14 adding local BLAST database support. This *requires* the matching update to the blast_datatypes repository. This adds basic wrappers for makeblastdb and blastdbinfo. This update includes work by Edward Kirton.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri Nov 09 06:53:55 2012 -0500
@@ -0,0 +1,121 @@
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.1">
+<description>Make BLAST database</description>
+<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="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>
+<requirements>
+    <requirement type="binary">makeblastdb</requirement>
+</requirements>
+<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/
+</help>
+</tool>