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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="assign_taxonomy" name="assign_taxonomy" version="1.2.0">
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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_tmpdir='$__new_file_path__'
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9 assign_taxonomy.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --assignment_method=$assign.assignment_method
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12 #if $assign.assignment_method = 'rdp'
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13 #if $assign.reference_seqs_fp != None
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14 --reference_seqs_fp=$assign.reference_seqs_fp
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15 #end if
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16 #if $assign.training_data_properties_fp != None
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17 --training_data_properties_fp=$assign.training_data_properties_fp
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18 #end if
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19 #if $assign.id_to_taxonomy_fp != None
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20 --id_to_taxonomy_fp=$assign.id_to_taxonomy_fp
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21 #end if
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22 --confidence=$confidence
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23 #elif $assign.assignment_method = 'blast'
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24 #if $assign.blast_ref.source = 'blast_db'
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25 --blast_db=$assign.blast_ref.blast_db
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26 #elif $assign.blast_ref.source = 'reference_seqs'
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27 --
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28 #end if
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29 --e_value=$assign.e_value
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30 --id_to_taxonomy_fp=$assign.id_to_taxonomy_fp
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31 #end if
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32 --output_dir=$__new_file_path__
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33 </command>
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34 <inputs>
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35 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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36 help="path to the input fasta file [REQUIRED]"/>
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37 <conditional name="assign">
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38 <param name="assignment_method" type="select" label="assignment_method"
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39 help="Taxon assignment method [default:rdp]">
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40 <option value="rdp" selected="true">rdp</option>
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41 <option value="blast">blast</option>
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42 </param>
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43 <when value="rdp">
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44 <param name="confidence" type="float" value="0.8" label="confidence"
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45 help="Minimum confidence to record an assignment, only used for rdp method [default: 0.8]"/>
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46 <param name="id_to_taxonomy_fp" type="data" format="rdp.taxonomy" optional="true" label="id_to_taxonomy_fp"
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47 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. "/>
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48 <param name="reference_seqs_fp" type="data" format="txt" optional="true" label="reference_seqs_fp"
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49 help="Reference sequences. For assignment with rdp, they are used as training sequences for the classifier."/>
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50 <param name="training_data_properties_fp" type="data" format="txt" optional="true" label="training_data_properties_fp"
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51 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')]"/>
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52 </when> <!-- rdp -->
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53 <when value="blast">
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54 <conditional name="blast_ref">
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55 <param name="source" type="select" label="blast database source">
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56 <option value="blast_db">blast database</option>
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57 <option value="reference_seqs">reference sequence fasta</option>
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58 </param>
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59 <when value="blast_db">
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60 <!-- chnage this to a select with built in blast targets -->
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61 <param name="blast_db" type="select" label="blast_db - Nucleotide BLAST database">
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62 <!-- The BLAST loc file has three columns:
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63 column 0 is an identifier (not used here, see legacy megablast wrapper),
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64 column 1 is the caption (show this to the user),
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65 column 2 is the database path (given to BLAST) -->
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66 <options from_file="blastdb.loc">
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67 <column name="name" index="1"/>
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68 <column name="value" index="2"/>
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69 </options>
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70 </param>
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71 </when> <!-- blast_db -->
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72 <when value="reference_seqs">
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73 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
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74 help="Reference sequences used to generate a blast database. "/>
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75 </when> <!-- reference_seqs -->
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76 </conditional> <!-- blast_ref -->
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77 <param name="e_value" type="float" value="0.001" label="e_value"
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78 help="Maximum e-value to record an assignment, only used for blast method [default: 0.001]"/>
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79 <param name="id_to_taxonomy_fp" type="data" format="seq.taxonomy" label="id_to_taxonomy_fp"
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80 help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a semicolon-separated list. "/>
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81 </when> <!-- blast -->
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82 </conditional> <!-- assign -->
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83 </inputs>
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84 <outputs>
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85 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: taxonomy"/>
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86 </outputs>
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87 <tests>
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88 </tests>
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89 <help>
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90
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91 </help>
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92 </tool>
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93