<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>