Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/assign_taxonomy.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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| 1 <tool id="assign_taxonomy" name="assign_taxonomy" version="2.0.0"> | |
| 2 <description>Assign taxonomy to each sequence</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">assign_taxonomy.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_outputdir='$outputfile.extra_files_path' | |
| 9 --galaxy_datasets='^\S+\.txt$:'$outputfile | |
| 10 assign_taxonomy.py | |
| 11 --input_fasta_fp=$input_fasta_fp | |
| 12 #if $id_to_taxonomy_fp != None and $id_to_taxonomy_fp.__str__ != 'None' and $id_to_taxonomy_fp.__str__ != '': | |
| 13 --id_to_taxonomy_fp=$id_to_taxonomy_fp | |
| 14 #end if | |
| 15 #if $reference_seqs_fp != None and $reference_seqs_fp.__str__ != 'None' and $reference_seqs_fp.__str__ != '': | |
| 16 --reference_seqs_fp=$reference_seqs_fp | |
| 17 #end if | |
| 18 #if $training_data_properties_fp != None and $training_data_properties_fp.__str__ != 'None' and $training_data_properties_fp.__str__ != '': | |
| 19 --training_data_properties_fp.$training_data_properties_fp | |
| 20 #end if | |
| 21 --confidence=$confidence | |
| 22 --assignment_method=rdp | |
| 23 --output_dir='$outputfile.extra_files_path' | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" | |
| 28 help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/> | |
| 29 <param name="confidence" type="float" value="0.8" label="confidence" | |
| 30 help="Minimum confidence to record an assignment, only used for rdp method [default: 0.8]"/> | |
| 31 <param name="id_to_taxonomy_fp" type="data" format="rdp.taxonomy" optional="true" label="id_to_taxonomy_fp" | |
| 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."/> | |
| 33 <param name="reference_seqs_fp" type="data" format="txt" optional="true" label="reference_seqs_fp" | |
| 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."/> | |
| 35 <param name="training_data_properties_fp" type="data" format="txt" optional="true" label="training_data_properties_fp" | |
| 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."/> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="txt" name="outputfile" metadata_source="input_fasta_fp"/> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 </tests> | |
| 43 <help>Only uses RDP. For blast, use MBAC blast tools. | |
| 44 | |
| 45 For more information, see assign_taxonomy_ in the Qiime documentation. | |
| 46 | |
| 47 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 48 | |
| 49 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 50 | |
| 51 .. _assign_taxonomy: http://qiime.org/scripts/assign_taxonomy.html</help> | |
| 52 </tool> | |
| 53 |