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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="identify_chimeric_seqs" name="identify_chimeric_seqs" version="1.2.0">
2 <description>Identify chimeric sequences in input FASTA file</description>
3 <requirements>
4 <requirement type="binary">identify_chimeric_seqs.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 identify_chimeric_seqs.py
9 --input_fasta_fp=$input_fasta_fp
10 #if $pick.chimera_detection_method == 'ChimeraSlayer':
11 --chimera_detection_method=$pick.chimera_detection_method
12 --aligned_reference_seqs_fp=$pick.aligned_reference_seqs_fp
13 --min_div_ratio=$pick.min_div_ratio
14 $pick.keep_intermediates
15 #elif $pick.chimera_detection_method == 'blast_fragments':
16 --chimera_detection_method=$pick.chimera_detection_method
17 --id_to_taxonomy_fp=$pick.id_to_taxonomy_fp
18 --reference_seqs_fp=$pick.reference_seqs_fp
19 --blast_db=$pick.blast_db
20 --num_fragments=$pick.num_fragments
21 --taxonomy_depth=$pick.taxonomy_depth
22 --max_e_value=$pick.max_e_value
23 #end if
24 --output_fp=$output_fp
25 </command>
26 <inputs>
27 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
28 help="path to the input fasta file [REQUIRED]"/>
29 <conditional name="pick">
30 <param name="chimera_detection_method" type="select" label="chimera_detection_method"
31 help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
32 <option value="blast_fragments">blast_fragments</option>
33 <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
34 </param>
35 <when value="ChimeraSlayer">
36 <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
37 help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
38 <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
39 help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value. [default: %default]"/>
40 <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
41 help="Keep intermediate files, useful for debugging [default: False]"/>
42 </when>
43 <when value="blast_fragments">
44 <param name="blast_db" type="text" label="blast_db"
45 help="Database to blast against. Must provide either --blast_db or --reference_seqs_fp when method is blast_fragments [default: ('NO', 'DEFAULT')]"/>
46 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
47 help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
48 <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
49 help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
50 <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
51 help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
52 <param name="num_fragments" type="integer" value="3" label="num_fragments"
53 help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
54 <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
55 help="Max e-value to assign taxonomy [default: 1e-30]"/>
56 </when>
57 </conditional> <!-- pick -->
58 </inputs>
59 <outputs>
60 <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: chimeras"/>
61 </outputs>
62 <tests>
63 </tests>
64 <help>
65
66 </help>
67 </tool>
68