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comparison amova.xml @ 0:0d34975c52a0 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 05:45:07 -0400
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1 <tool profile="16.07" id="mothur_amova" name="Amova" version="@WRAPPER_VERSION@.0">
2 <description>Analysis of molecular variance</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 'amova(
17 phylip=dist.dat,
18 iters=$iters,
19 alpha=$alpha,
20 #if $sets:
21 sets=$sets,
22 #end if
23 design=design.dat
24 )'
25 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur
27 | tee mothur.out.log
28 ]]></command>
29 <inputs>
30 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
31 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/>
32 <param name="alpha" type="float" optional="true" min="0" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/>
33 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
34 <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze." help="The set names are separated by dashes. The defualt is all sets in designfile">
35 <options>
36 <filter type="data_meta" ref="design" key="sets"/>
37 </options>
38 </param>
39 </inputs>
40 <outputs>
41 <expand macro="logfile-output"/>
42 <data name="amova" format="tabular" from_work_dir="dist.amova" label="${tool.name} on ${on_string}: amova"/>
43 </outputs>
44 <tests>
45 <test>
46 <param name="dist" value="amazon.dist"/>
47 <param name="design" value="amazon.design"/>
48 <output name="amova" ftype="tabular">
49 <assert_contents>
50 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/>
51 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
52 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
53 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/>
54 <has_text text="p-value"/>
55 </assert_contents>
56 </output>
57 <expand macro="logfile-test"/>
58 </test>
59 </tests>
60 <help>
61 <![CDATA[
62
63 @MOTHUR_OVERVIEW@
64
65 **Command Documentation**
66
67 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations.
68
69 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
70 ======= =======
71 duck bird
72 cow mammal
73 pig mammal
74 goose bird
75 cobra reptile
76 ======= =======
77
78 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
79
80
81 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
82 .. _amova: https://www.mothur.org/wiki/Amova
83
84 ]]>
85 </help>
86 <expand macro="citations"/>
87 </tool>