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