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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="align_seqs" name="align_seqs" version="1.2.0">
2 <description>Align sequences using a variety of alignment methods</description>
3 <requirements>
4 <requirement type="binary">align_seqs.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_outputdir='$log.extra_files_path'
9 --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures
10 align_seqs.py
11 --input_fasta_fp=$input_fasta_fp
12 --alignment_method=$align.alignment_method
13 #if $align.alignment_method == 'pynast':
14 --template_fp=$align.alignment.template_fp
15 --pairwise_alignment_method=$align.pairwise_alignment_method
16 --min_length=$align.min_length
17 --min_percent_id=$align.min_percent_id
18 --blast_db=$align.blast_db
19 #elif $align.alignment_method == 'infernal':
20 --template_fp=$align.alignment.template_fp
21 #elif $align.alignment_method == 'clustalw':
22 #echo ''
23 #elif $align.alignment_method == 'muscle':
24 #echo ''
25 #elif $align.alignment_method == 'mafft':
26 #echo ''
27 #end if
28
29 --output_dir='$log.extra_files_path'
30 </command>
31 <inputs>
32 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
33 help="path to the input fasta file [REQUIRED]"/>
34
35 <conditional name="align">
36 <param name="alignment_method" type="select" label="alignment_method"
37 help="Method for aligning sequences. Valid choices are: pynast, infernal, clustalw, muscle, infernal, mafft [default: pynast]">
38 <option value="pynast" selected="true">pynast</option>
39 <option value="infernal">infernal</option>
40 <option value="clustalw">clustalw</option>
41 <option value="muscle">muscle</option>
42 <option value="mafft">mafft</option>
43 </param>
44
45 <when value="pynast">
46 <conditional name="alignment">
47 <param name="source" type="select" label="Select Template from" help="">
48 <option value="hist">History</option>
49 <option value="ref">Cached Reference</option>
50 </param>
51 <when value="ref">
52 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
53 <options from_file="mothur_aligndb.loc">
54 <column name="name" index="0" />
55 <column name="value" index="1" />
56 </options>
57 </param>
58 </when>
59 <when value="hist">
60 <param name="template_fp" type="data" format="txt" label="template_fp"
61 help="Filepath for template against [REQUIRED if for alignment_method pynast or infernal]"/>
62 </when>
63 </conditional>
64 <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
65 help="method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [default: uclust]">
66 <option value="muscle">muscle</option>
67 <option value="pair_hmm">pair_hmm</option>
68 <option value="clustal">clustal</option>
69 <option value="blast">blast</option>
70 <option value="uclust" selected="true">uclust</option>
71 <option value="mafft">mafft</option>
72 </param>
73 <param name="min_length" type="integer" value="150" label="min_length"
74 help="Minimum sequence length to include in alignment [default: 150]"/>
75 <param name="min_percent_id" type="float" value="0.75" label="min_percent_id"
76 help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
77 <param name="blast_db" type="text" label="blast_db" optional="true"
78 help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
79 </when> <!-- pynast -->
80
81 <when value="infernal">
82 <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
83 <conditional name="alignment">
84 <param name="source" type="select" label="Select Template from" help="">
85 <option value="hist">History</option>
86 <option value="ref">Cached Reference</option>
87 </param>
88 <when value="ref">
89 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
90 <options from_file="mothur_aligndb.loc">
91 <column name="name" index="0" />
92 <column name="value" index="1" />
93 </options>
94 </param>
95 </when>
96 <when value="hist">
97 <param name="template_fp" type="data" format="txt" label="template_fp"
98 help="Filepath for template against [REQUIRED if for alignment_method pynast or infernal]"/>
99 </when>
100 </conditional>
101 </when> <!-- infernal -->
102
103 <when value="clustalw">
104 </when> <!-- clustalw -->
105 <when value="muscle">
106 </when> <!-- muscle -->
107 <when value="mafft">
108 </when> <!-- mafft -->
109
110 </conditional> <!-- align -->
111
112
113 </inputs>
114 <outputs>
115 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
116 <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
117 <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" >
118 <filter>align['alignment_method'] == 'pynast'</filter>
119 </data>
120 </outputs>
121 <tests>
122 </tests>
123 <help>
124
125 </help>
126 </tool>
127