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comparison libshuff.xml @ 0:590cb2451872 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 05:22:17 -0400
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-1:000000000000 0:590cb2451872
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat &&
14 ln -s "$group" group.dat &&
15
16 echo 'libshuff(
17 phylip=dist.dat,
18 group=group.dat,
19 #if $groups:
20 groups=${ str($groups).replace(",","-") },
21 #end if
22 sim=$sim,
23 #if $form.form2 == "discrete":
24 step=$form.step,
25 #if $form.cutoff:
26 cutoff=$form.cutoff,
27 #end if
28 #end if
29 iters=$iters
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 | tee mothur.out.log
34 ]]></command>
35 <inputs>
36 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
37 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
38 <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
39 <options>
40 <filter type="data_meta" ref="group" key="groups"/>
41 </options>
42 </param>
43 <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
44 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
45 <conditional name="form">
46 <param name="form2" type="select" label="form - Select a Clustering Method" help="">
47 <option value="integral" selected="true">Integral</option>
48 <option value="discrete">Discrete</option>
49 </param>
50 <when value="integral"/>
51 <when value="discrete">
52 <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
53 <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
54 </when>
55 </conditional>
56 </inputs>
57 <outputs>
58 <expand macro="logfile-output"/>
59 <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
60 <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>
61 </outputs>
62 <tests>
63 <test>
64 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
65 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
66 <output name="summary">
67 <assert_contents>
68 <has_text text="forest-pasture"/>
69 <has_text text="pasture-forest"/>
70 </assert_contents>
71 </output>
72 <output name="coverage">
73 <assert_contents>
74 <has_text text="dist"/>
75 <has_text text="forest-pasture"/>
76 <has_text text="pasture-forest"/>
77 </assert_contents>
78 </output>
79 <expand macro="logfile-test"/>
80 </test>
81 <test>
82 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
83 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
84 <param name="groups" value="forest,pasture"/>
85 <param name="form2" value="discrete"/>
86 <param name="step" value="0.25"/>
87 <param name="cutoff" value="0.25"/>
88 <output name="summary">
89 <assert_contents>
90 <has_text text="forest-pasture"/>
91 <has_text text="pasture-forest"/>
92 </assert_contents>
93 </output>
94 <output name="coverage">
95 <assert_contents>
96 <has_text text="dist"/>
97 <has_text text="forest-pasture"/>
98 <has_text text="pasture-forest"/>
99 </assert_contents>
100 </output>
101 <expand macro="logfile-test"/>
102 </test>
103 </tests>
104 <help>
105 <![CDATA[
106
107 @MOTHUR_OVERVIEW@
108
109
110 **Command Documentation**
111
112 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.
113
114 .. _libshuff: https://www.mothur.org/wiki/Libshuff
115
116 ]]>
117 </help>
118 <expand macro="citations"/>
119 </tool>