--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assign_taxonomy.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,93 @@
+<tool id="assign_taxonomy" name="assign_taxonomy" version="1.2.0">
+ <description>Assign taxonomy to each sequence</description>
+ <requirements>
+  <requirement type="binary">assign_taxonomy.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  assign_taxonomy.py
+  --input_fasta_fp=$input_fasta_fp
+  --assignment_method=$assign.assignment_method
+  #if $assign.assignment_method = 'rdp'
+   #if $assign.reference_seqs_fp != None
+    --reference_seqs_fp=$assign.reference_seqs_fp
+   #end if
+   #if $assign.training_data_properties_fp != None
+    --training_data_properties_fp=$assign.training_data_properties_fp
+   #end if
+   #if $assign.id_to_taxonomy_fp != None
+    --id_to_taxonomy_fp=$assign.id_to_taxonomy_fp
+   #end if
+   --confidence=$confidence
+  #elif $assign.assignment_method = 'blast'
+   #if $assign.blast_ref.source = 'blast_db'
+    --blast_db=$assign.blast_ref.blast_db
+   #elif $assign.blast_ref.source = 'reference_seqs'
+    --
+   #end if
+   --e_value=$assign.e_value
+   --id_to_taxonomy_fp=$assign.id_to_taxonomy_fp
+  #end if
+  --output_dir=$__new_file_path__
+ </command>
+ <inputs>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="path to the input fasta file [REQUIRED]"/>
+  <conditional name="assign">
+    <param name="assignment_method" type="select" label="assignment_method"
+     help="Taxon assignment method [default:rdp]">
+      <option value="rdp" selected="true">rdp</option>
+      <option value="blast">blast</option>
+    </param>
+    <when value="rdp">
+     <param name="confidence" type="float" value="0.8" label="confidence"
+      help="Minimum confidence to record an assignment, only used for rdp method [default: 0.8]"/>
+     <param name="id_to_taxonomy_fp" type="data" format="rdp.taxonomy" optional="true" label="id_to_taxonomy_fp"
+      help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep. "/>
+     <param name="reference_seqs_fp" type="data" format="txt" optional="true" label="reference_seqs_fp"
+      help="Reference sequences.  For assignment with rdp, they are used as training sequences for the classifier."/>
+     <param name="training_data_properties_fp" type="data" format="txt" optional="true" label="training_data_properties_fp"
+      help="Path to '.properties' file in pre-compiled training data for the RDP Classifier.  This option is overridden by the -t and -r options. [default: ('NO', 'DEFAULT')]"/>
+    </when> <!-- rdp -->
+    <when value="blast">
+     <conditional name="blast_ref">
+      <param name="source" type="select" label="blast database source">
+       <option value="blast_db">blast database</option>
+       <option value="reference_seqs">reference sequence fasta</option>
+      </param>
+      <when value="blast_db">
+       <!-- chnage this to a select with built in blast targets -->
+       <param name="blast_db" type="select" label="blast_db - Nucleotide BLAST database">
+        <!-- The BLAST loc file has three columns:
+         column 0 is an identifier (not used here, see legacy megablast wrapper),
+         column 1 is the caption (show this to the user),
+         column 2 is the database path (given to BLAST) -->
+        <options from_file="blastdb.loc">
+         <column name="name" index="1"/>
+         <column name="value" index="2"/>
+        </options>
+       </param>
+      </when> <!-- blast_db -->
+      <when value="reference_seqs">
+       <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
+        help="Reference sequences used to generate a blast database. "/>
+      </when> <!-- reference_seqs -->
+     </conditional> <!-- blast_ref -->
+     <param name="e_value" type="float" value="0.001" label="e_value"
+      help="Maximum e-value to record an assignment, only used for blast method [default: 0.001]"/>
+     <param name="id_to_taxonomy_fp" type="data" format="seq.taxonomy" label="id_to_taxonomy_fp"
+      help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a semicolon-separated list. "/>
+    </when> <!-- blast -->
+ </conditional> <!-- assign -->
+ </inputs>
+ <outputs>
+  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: taxonomy"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+