<tool id="assign_taxonomy" name="assign_taxonomy" version="2.0.0">
 <description>Assign taxonomy to each sequence</description>
 <requirements>
  <requirement type="binary">assign_taxonomy.py</requirement>
 </requirements>
 <command interpreter="python">
 qiime_wrapper.py
 --galaxy_outputdir='$outputfile.extra_files_path'
 --galaxy_datasets='^\S+\.txt$:'$outputfile
 assign_taxonomy.py
 --input_fasta_fp=$input_fasta_fp
 #if $id_to_taxonomy_fp != None and $id_to_taxonomy_fp.__str__ != 'None' and $id_to_taxonomy_fp.__str__ != '':
 --id_to_taxonomy_fp=$id_to_taxonomy_fp
 #end if
 #if $reference_seqs_fp != None and $reference_seqs_fp.__str__ != 'None' and $reference_seqs_fp.__str__ != '':
 --reference_seqs_fp=$reference_seqs_fp
 #end if
 #if $training_data_properties_fp != None and $training_data_properties_fp.__str__ != 'None' and $training_data_properties_fp.__str__ != '':
 --training_data_properties_fp.$training_data_properties_fp
 #end if
 --confidence=$confidence
 --assignment_method=rdp
 --output_dir='$outputfile.extra_files_path'
 </command>
 
 <inputs>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
   help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
  <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. If you upload an id-to-taxonomy-file, you must also a refseq file."/>
  <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. If you upload a refseq, you must also upload an id-to-taxonomy file."/>
  <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 id-to-taxonomy file and the refseqs file."/>
 </inputs>
 <outputs>
  <data format="txt" name="outputfile" metadata_source="input_fasta_fp"/>
 </outputs>
 <tests>
 </tests>
 <help>Only uses RDP. For blast, use MBAC blast tools.
 
For more information, see assign_taxonomy_ in the Qiime documentation.
 
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _assign_taxonomy: http://qiime.org/scripts/assign_taxonomy.html</help>
</tool>