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comparison libshuff.xml @ 0:73a96aeacf46 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:36:17 -0400
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1 <tool profile="16.07" id="mothur_libshuff" name="Libshuff" version="@WRAPPER_VERSION@.0">
2 <description>Cramer-von Mises tests communities for the same structure</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$dist" dist.dat &&
11 ln -s "$group" group.dat &&
12
13 echo 'libshuff(
14 phylip=dist.dat,
15 group=group.dat,
16 #if $groups:
17 groups=${ str($groups).replace(",","-") },
18 #end if
19 sim=$sim,
20 #if $form.form2 == "discrete":
21 step=$form.step,
22 #if $form.cutoff:
23 cutoff=$form.cutoff,
24 #end if
25 #end if
26 iters=$iters
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 ]]></command>
31 <inputs>
32 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
33 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
34 <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
35 <options>
36 <filter type="data_meta" ref="group" key="groups"/>
37 </options>
38 </param>
39 <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
40 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
41 <conditional name="form">
42 <param name="form2" type="select" label="form - Select a Clustering Method" help="">
43 <option value="integral" selected="true">Integral</option>
44 <option value="discrete">Discrete</option>
45 </param>
46 <when value="integral"/>
47 <when value="discrete">
48 <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
49 <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
50 </when>
51 </conditional>
52 </inputs>
53 <outputs>
54 <expand macro="logfile-output"/>
55 <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
56 <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>
57 </outputs>
58 <tests>
59 <test>
60 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
61 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
62 <output name="summary">
63 <assert_contents>
64 <has_text text="forest-pasture"/>
65 <has_text text="pasture-forest"/>
66 </assert_contents>
67 </output>
68 <output name="coverage">
69 <assert_contents>
70 <has_text text="dist"/>
71 <has_text text="forest-pasture"/>
72 <has_text text="pasture-forest"/>
73 </assert_contents>
74 </output>
75 <expand macro="logfile-test"/>
76 </test>
77 <test>
78 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
79 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
80 <param name="groups" value="forest,pasture"/>
81 <param name="form2" value="discrete"/>
82 <param name="step" value="0.25"/>
83 <param name="cutoff" value="0.25"/>
84 <output name="summary">
85 <assert_contents>
86 <has_text text="forest-pasture"/>
87 <has_text text="pasture-forest"/>
88 </assert_contents>
89 </output>
90 <output name="coverage">
91 <assert_contents>
92 <has_text text="dist"/>
93 <has_text text="forest-pasture"/>
94 <has_text text="pasture-forest"/>
95 </assert_contents>
96 </output>
97 <expand macro="logfile-test"/>
98 </test>
99 </tests>
100 <help>
101 <![CDATA[
102
103 @MOTHUR_OVERVIEW@
104
105
106 **Command Documenation**
107
108 The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.
109
110 .. _libshuff: http://www.mothur.org/wiki/Libshuff
111
112 ]]>
113 </help>
114 <expand macro="citations"/>
115 </tool>