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comparison qiime/align_seqs.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="align_seqs" name="align_seqs" version="2.0.0">
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=$alignment_method
13 #if $alignment_method.__str__ == 'pynast':
14 #if $alignment.template_fp != None and $alignment.template_fp.__str__ != 'None' and $alignment.template_fp.__str__ != '':
15 --template_fp=$alignment.template_fp
16 #end if
17 --pairwise_alignment_method=$pairwise_alignment_method
18 --min_length=$min_length
19 --min_percent_id=$min_percent_id
20 #if $blast_db != None and $blast_db.__str__ != 'None' and $blast_db.__str__ != '':
21 --blast_db=$blast_db
22 #end if
23 #elif $alignment_method.__str__ == 'infernal':
24 --template_fp=$alignment.template_fp
25 #end if
26
27 --output_dir='$log.extra_files_path'
28 </command>
29 <inputs>
30 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
31 <param name="alignment_method" type="select" label="alignment_method"
32 help="Method for aligning sequences. [default: pynast]">
33 <option value="pynast" selected="true">pynast</option>
34 <option value="infernal">infernal</option>
35 <option value="clustalw">clustalw</option>
36 <option value="muscle">muscle</option>
37 <option value="mafft">mafft</option>
38 </param>
39 <conditional name="alignment">
40 <param name="source" type="select" label="Select Template from" help="">
41 <option value="hist">History</option>
42 <option value="ref">Cached Reference</option>
43 </param>
44 <when value="ref">
45 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
46 <options>
47 <column name="name" index="0" />
48 <column name="value" index="1" />
49 </options>
50 </param>
51 </when>
52 <when value="hist">
53 <param name="template_fp" type="data" format="txt" label="template_fp" optional="true"
54 help="Filepath for template against [REQUIRED ONLY if for alignment_method pynast or infernal]"/>
55 </when>
56 </conditional> <!--alignment-->
57 <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
58 help="Method for performing pairwise alignment; only required for PyNAST. [default: uclust]">
59 <option value="muscle">muscle</option>
60 <option value="pair_hmm">pair_hmm</option>
61 <option value="clustal">clustal</option>
62 <option value="blast">blast</option>
63 <option value="uclust" selected="true">uclust</option>
64 <option value="mafft">mafft</option>
65 </param>
66 <param name="min_length" type="integer" optional="true" value="150" label="min_length"
67 help="Minimum sequence length to include in alignment [default: 150]"/>
68 <param name="min_percent_id" type="float" value="0.75" optional="true" label="min_percent_id"
69 help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
70 <param name="blast_db" type="data" format="txt" label="blast_db" optional="true"
71 help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
72 <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
73
74 </inputs>
75 <outputs>
76 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
77 <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
78 <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" />
79 </outputs>
80 <tests>
81 </tests>
82 <help> .. class:: warningmark
83 Note: MUSCLE alignment is still not verified. Use at your own risk.
84
85 For more information, see align_seqs_ in the Qiime documentation.
86
87 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
88
89 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
90
91 .. _align_seqs: http://qiime.org/scripts/align_seqs.html</help>
92 </tool>
93