--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/assign_taxonomy.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,53 @@
+<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>
+