Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/mantel.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 |
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children | 49058b1f8d3f |
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1 <tool id="mothur_mantel" name="Mantel" version="1.19.0"> | |
2 <description>Mantel correlation coefficient between two matrices.</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='mantel' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.mantel$:'$mantel | |
7 --outputdir='$logfile.extra_files_path' | |
8 --phylip=$dist | |
9 --phylip2=$dist2 | |
10 --method=$method | |
11 #if int($iters.__str__) > 0: | |
12 --iters=$iters | |
13 #end if | |
14 </command> | |
15 <inputs> | |
16 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> | |
17 <param name="dist2" type="data" format="lower.dist,square.dist" label="phylip2 - Distance Matrix"/> | |
18 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson" > | |
19 <option value="pearson" selected="true">pearson</option> | |
20 <option value="spearman">spearman</option> | |
21 <option value="kendall">kendall</option> | |
22 </param> | |
23 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
27 <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/> | |
28 </outputs> | |
29 <requirements> | |
30 <requirement type="binary">mothur</requirement> | |
31 </requirements> | |
32 <tests> | |
33 </tests> | |
34 <help> | |
35 **Mothur Overview** | |
36 | |
37 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
38 in the Department of Microbiology and Immunology at The University of Michigan, | |
39 provides bioinformatics for the microbial ecology community. | |
40 | |
41 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
42 | |
43 **Command Documenation** | |
44 | |
45 The mantel_ command calculates the Mantel correlation coefficient between two matrices_. | |
46 | |
47 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix | |
48 .. _mantel: http://www.mothur.org/wiki/Mantel | |
49 | |
50 | |
51 </help> | |
52 </tool> |