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1 <tool id="assign_taxonomy" name="assign_taxonomy" version="2.0.0">
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2 <description>Assign taxonomy to each sequence</description>
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3 <requirements>
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4 <requirement type="binary">assign_taxonomy.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_outputdir='$outputfile.extra_files_path'
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9 --galaxy_datasets='^\S+\.txt$:'$outputfile
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10 assign_taxonomy.py
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11 --input_fasta_fp=$input_fasta_fp
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12 #if $id_to_taxonomy_fp != None and $id_to_taxonomy_fp.__str__ != 'None' and $id_to_taxonomy_fp.__str__ != '':
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13 --id_to_taxonomy_fp=$id_to_taxonomy_fp
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14 #end if
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15 #if $reference_seqs_fp != None and $reference_seqs_fp.__str__ != 'None' and $reference_seqs_fp.__str__ != '':
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16 --reference_seqs_fp=$reference_seqs_fp
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17 #end if
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18 #if $training_data_properties_fp != None and $training_data_properties_fp.__str__ != 'None' and $training_data_properties_fp.__str__ != '':
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19 --training_data_properties_fp.$training_data_properties_fp
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20 #end if
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21 --confidence=$confidence
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22 --assignment_method=rdp
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23 --output_dir='$outputfile.extra_files_path'
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24 </command>
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25
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26 <inputs>
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27 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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28 help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
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29 <param name="confidence" type="float" value="0.8" label="confidence"
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30 help="Minimum confidence to record an assignment, only used for rdp method [default: 0.8]"/>
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31 <param name="id_to_taxonomy_fp" type="data" format="rdp.taxonomy" optional="true" label="id_to_taxonomy_fp"
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32 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."/>
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33 <param name="reference_seqs_fp" type="data" format="txt" optional="true" label="reference_seqs_fp"
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34 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."/>
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35 <param name="training_data_properties_fp" type="data" format="txt" optional="true" label="training_data_properties_fp"
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36 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."/>
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37 </inputs>
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38 <outputs>
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39 <data format="txt" name="outputfile" metadata_source="input_fasta_fp"/>
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40 </outputs>
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41 <tests>
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42 </tests>
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43 <help>Only uses RDP. For blast, use MBAC blast tools.
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44
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45 For more information, see assign_taxonomy_ in the Qiime documentation.
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46
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47 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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48
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49 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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50
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51 .. _assign_taxonomy: http://qiime.org/scripts/assign_taxonomy.html</help>
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52 </tool>
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53
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