Mercurial > repos > iuc > mothur_libshuff

comparison libshuff.xml @ 3:8b4214eada86 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:17:48 -0500
parents a84c121a3b75
children af1dd82c53bb
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2:47e724ed0fe4 3:8b4214eada86
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat && 13 ln -s '$dist' dist.dat &&
14 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 15
16 echo 'libshuff( 16 echo 'libshuff(
17 phylip=dist.dat, 17 phylip=dist.dat,
18 group=group.dat, 18 group=group.dat,
19 #if $groups: 19 #if $groups:
20 groups=${ str($groups).replace(",","-") }, 20 groups=${ str($groups).replace(",","-") },
21 #end if 21 #end if
22 sim=$sim, 22 sim=$sim,
23 #if $form.form2 == "discrete": 23 #if $form.form2 == "discrete":
24 step=$form.step, 24 step=$form.step,
25 #if $form.cutoff: 25 #if $form.cutoff:
26 cutoff=$form.cutoff, 26 cutoff=$form.cutoff,
27 #end if 27 #end if
28 #end if 28 #end if
29 iters=$iters 29 iters=$iters
30 )' 30 )'
31 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 32 | mothur
33 | tee mothur.out.log 33 | tee mothur.out.log
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 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"/> 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"> 38 <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
99 </assert_contents> 99 </assert_contents>
100 </output> 100 </output>
101 <expand macro="logfile-test"/> 101 <expand macro="logfile-test"/>
102 </test> 102 </test>
103 </tests> 103 </tests>
104 <help> 104 <help><![CDATA[
105 <![CDATA[
106 105
107 @MOTHUR_OVERVIEW@ 106 @MOTHUR_OVERVIEW@
108 107
109 108
110 **Command Documentation** 109 **Command Documentation**
111 110
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. 111 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.
113 112
114 .. _libshuff: https://www.mothur.org/wiki/Libshuff 113 .. _libshuff: https://www.mothur.org/wiki/Libshuff
115 114
116 ]]> 115 ]]></help>
117 </help>
118 <expand macro="citations"/> 116 <expand macro="citations"/>
119 </tool> 117 </tool>