Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/align.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 4f797d3eee3a |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_align_seqs" name="Align.seqs" version="1.16.0"> | 1 <tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0"> |
2 <description>Align sequences to a template alignment</description> | 2 <description>Align sequences to a template alignment</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='align.seqs' | 5 --cmd='align.seqs' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align$:'$out_file,'^\S+\.align\.report$:'$report | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align$:'$out_file,'^\S+\.align\.report$:'$report |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --candidate=$candidate | 8 --fasta=$candidate |
9 --template=$alignment.template | 9 --reference=$alignment.template |
10 #if $search.method == 'kmer': | 10 #if $search.method == 'kmer': |
11 --ksize=$search.ksize | 11 --ksize=$search.ksize |
12 #else: | 12 #else: |
13 --search=$search.method | 13 --search=$search.method |
14 #end if | 14 #end if |
24 --threshold=$reverse.threshold | 24 --threshold=$reverse.threshold |
25 #end if | 25 #end if |
26 --processors=2 | 26 --processors=2 |
27 </command> | 27 </command> |
28 <inputs> | 28 <inputs> |
29 <param name="candidate" type="data" format="fasta" label="candidate - Candiate Sequences"/> | 29 <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
30 <conditional name="alignment"> | 30 <conditional name="alignment"> |
31 <param name="source" type="select" label="Select Template from" help=""> | 31 <param name="source" type="select" label="Select Reference Template from" help=""> |
32 <option value="hist">History</option> | |
33 <option value="ref">Cached Reference</option> | 32 <option value="ref">Cached Reference</option> |
33 <option value="history">Your History</option> | |
34 </param> | 34 </param> |
35 <when value="ref"> | 35 <when value="ref"> |
36 <param name="template" type="select" label="template - Select an alignment database " help=""> | 36 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
37 <options from_file="mothur_aligndb.loc"> | 37 <options from_file="mothur_aligndb.loc"> |
38 <column name="name" index="0" /> | 38 <column name="name" index="0" /> |
39 <column name="value" index="1" /> | 39 <column name="value" index="1" /> |
40 </options> | 40 </options> |
41 </param> | 41 </param> |
42 </when> | 42 </when> |
43 <when value="hist"> | 43 <when value="history"> |
44 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> | 44 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
45 </when> | 45 </when> |
46 </conditional> | 46 </conditional> |
47 <conditional name="search"> | 47 <conditional name="search"> |
48 <param name="method" type="select" label="Select a search method" help=""> | 48 <param name="method" type="select" label="Select a search method" help=""> |
49 <option value="kmer">kmer (default)</option> | 49 <option value="kmer">kmer (default)</option> |
109 | 109 |
110 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 110 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
111 | 111 |
112 **Command Documenation** | 112 **Command Documenation** |
113 | 113 |
114 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template alignment. | 114 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_. |
115 | 115 |
116 The general approach is to | |
117 i) find the closest template for each candidate using kmer searching, blastn, or suffix tree searching; | |
118 ii) to make a pairwise alignment between the candidate and de-gapped template sequences using the Needleman-Wunsch, Gotoh, or blastn algorithms; and | |
119 iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment. | |
120 | |
121 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure. | |
122 | |
123 .. _template_alignment: http://www.mothur.org/wiki/Alignment_database | |
116 .. _align.seqs: http://www.mothur.org/wiki/Align.seqs | 124 .. _align.seqs: http://www.mothur.org/wiki/Align.seqs |
117 | 125 |
118 | 126 |
119 </help> | 127 </help> |
120 </tool> | 128 </tool> |