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comparison otu_clustering/cluster_otu.xml @ 0:52043d3d71f5 draft

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author qfab
date Wed, 28 May 2014 21:22:08 -0400
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1 <tool id="cluster_otu" name="Cluster OTU" version="1.0.0">
2 <description>Cluster OTUs</description>
3 <command>
4 usearch -cluster_otus $input -otus $output -otuid $radius 2&gt;1
5 </command>
6
7 <inputs>
8 <param name="input" type="data" format="fasta" label="Input sequence file"
9 help="Size annotation is required, see description below!"/>
10 <param name="radius" type='float' value='0.97' label='Minimum cluster radius'
11 help="default=0.97, corresponds to minimum of 97% sequence identity" />
12 </inputs>
13
14 <outputs>
15 <data name='output' format="fasta" />
16 </outputs>
17
18 <help>
19 ===========
20 Description
21 ===========
22
23 Performs OTU clustering using the USEARCH-Tool-Suite_.
24
25 .. _USEARCH-Tool-Suite: http://www.drive5.com/usearch/
26
27 -----
28
29 -----
30 Input
31 -----
32
33 FASTA file with size annotation in the input line, e.g. >sequenceXXXX;size=1443;
34
35 .. class:: warningmark
36
37 Size annotation is required.
38
39 ----------
40 Parameters
41 ----------
42
43 radius
44 (Usearch v7.0.1002 and earlier) specifies the OTU 'radius' as the minimum identity between an OTU member sequence and the representative sequence as a fractional identity 0.0 to 1.0. Default is 0.97, which corresponds to a minimum identity of 97%.
45
46 ------
47 Output
48 ------
49
50 FASTA output of the representative sequences.
51
52 .. class:: warningmark
53
54 If there is a "size=XX" annotation in the identifier line of the output file, please note this is NOT the number of sequences in this cluster. The size annotation is then coming from the input file.
55
56 -----
57
58 =========
59 Resources
60 =========
61
62 UPARSE_ (OTU Clustering)
63
64 .._UPARSE: http://drive5.com/usearch/manual/cluster_otus.html
65
66 **Author**
67
68 Robert C. Edgar (bob@drive5.com)
69
70 **Wrapper Author**
71
72 QFAB Bioinformatics (support@qfab.org)
73 </help>
74 <tests>
75 <test>
76 <param name="input" value="seqs_derep.fasta" />
77 <param name="radius" value="0.97" />
78 <output name="output" file="seqs_otus.fasta" ftype="fasta" lines_diff="10" />
79 </test>
80 </tests>
81 </tool>