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comparison anosim.xml @ 0:08ccc12f2a3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:39:40 -0400
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-1:000000000000 0:08ccc12f2a3a
1 <tool profile="16.07" id="mothur_anosim" name="Anosim" version="@WRAPPER_VERSION@.0">
2 <description>Non-parametric multivariate analysis of changes in community structure</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat &&
14 ln -s "$design" design.dat &&
15
16 echo 'anosim(
17 phylip=dist.dat,
18 iters=$iters,
19 alpha=$alpha,
20 design=design.dat
21 )'
22 | sed 's/ //g' ## mothur trips over whitespace
23 | mothur
24 | tee mothur.out.log
25 ]]></command>
26 <inputs>
27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
28 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
29 <param name="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision (default 0.05)"/>
30 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
31 </inputs>
32 <outputs>
33 <expand macro="logfile-output"/>
34 <data name="anosim" format="tabular" from_work_dir="dist.anosim" label="${tool.name} on ${on_string}: anosim"/>
35 </outputs>
36 <tests>
37 <test>
38 <param name="dist" value="amazon.dist"/>
39 <param name="design" value="amazon.design"/>
40 <output name="anosim" ftype="tabular">
41 <assert_contents>
42 <has_line_matching expression="^comparison\tR-value\tP-value$"/>
43 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
44 </assert_contents>
45 </output>
46 <expand macro="logfile-test"/>
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51
52 @MOTHUR_OVERVIEW@
53
54 **Command Documentation**
55
56 The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure.
57
58 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
59 ======= =======
60 duck bird
61 cow mammal
62 pig mammal
63 goose bird
64 cobra reptile
65 ======= =======
66
67 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
68
69
70 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
71 .. _anosim: https://www.mothur.org/wiki/Anosim
72
73 ]]>
74 </help>
75 <expand macro="citations"/>
76 </tool>