Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/anosim.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
---|---|
date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | |
children | 49058b1f8d3f |
comparison
equal
deleted
inserted
replaced
1:fcc0778f6987 | 2:e990ac8a0f58 |
---|---|
1 <tool id="mothur_anosim" name="Anosim" version="1.19.0"> | |
2 <description>Non-parametric multivariate analysis of changes in community structure</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='anosim' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.anosim$:'$anosim | |
7 --outputdir='$logfile.extra_files_path' | |
8 --phylip=$dist | |
9 --design=$design | |
10 #if int($iters.__str__) > 0: | |
11 --iters=$iters | |
12 #end if | |
13 #if float($alpha.__str__) > 0.0: | |
14 --alpha=$alpha | |
15 #end if | |
16 </command> | |
17 <inputs> | |
18 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> | |
19 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" | |
20 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> | |
21 <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> | |
22 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> | |
23 </inputs> | |
24 <outputs> | |
25 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
26 <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/> | |
27 </outputs> | |
28 <requirements> | |
29 <requirement type="binary">mothur</requirement> | |
30 </requirements> | |
31 <tests> | |
32 </tests> | |
33 <help> | |
34 **Mothur Overview** | |
35 | |
36 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
37 in the Department of Microbiology and Immunology at The University of Michigan, | |
38 provides bioinformatics for the microbial ecology community. | |
39 | |
40 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
41 | |
42 **Command Documenation** | |
43 | |
44 The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure. | |
45 | |
46 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : | |
47 ======= ======= | |
48 duck bird | |
49 cow mammal | |
50 pig mammal | |
51 goose bird | |
52 cobra reptile | |
53 ======= ======= | |
54 | |
55 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. | |
56 | |
57 | |
58 .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix | |
59 .. _anosim: http://www.mothur.org/wiki/Anosim | |
60 | |
61 | |
62 </help> | |
63 </tool> |