Mercurial > repos > iuc > mothur_libshuff

annotate libshuff.xml @ 5:eefbe872fd04 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:26:19 -0400
parents ffe8649e5434
children 1e4687170395
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590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_libshuff" name="Libshuff" version="@WRAPPER_VERSION@.0">
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Cramer-von Mises tests communities for the same structure</description>
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3 <macros>
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4 <import>macros.xml</import>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$dist' dist.dat &&
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$group' group.dat &&
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15
2
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16 echo 'libshuff(
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 phylip=dist.dat,
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 group=group.dat,
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #if $groups:
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20 groups=${ str($groups).replace(",","-") },
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #end if
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 sim=$sim,
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #if $form.form2 == "discrete":
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 step=$form.step,
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #if $form.cutoff:
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 cutoff=$form.cutoff,
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 #end if
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #end if
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 iters=$iters
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 )'
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 | sed 's/ //g' ## mothur trips over whitespace
ffe8649e5434 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 | mothur
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33 | tee mothur.out.log
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590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 ]]></command>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 <inputs>
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36 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <options>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <filter type="data_meta" ref="group" key="groups"/>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 </options>
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42 </param>
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43 <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
590cb2451872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
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45 <conditional name="form">
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46 <param name="form2" type="select" label="form - Select a Clustering Method" help="">
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47 <option value="integral" selected="true">Integral</option>
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48 <option value="discrete">Discrete</option>
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49 </param>
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50 <when value="integral"/>
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51 <when value="discrete">
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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"/>
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53 <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
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54 </when>
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55 </conditional>
2
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56 <expand macro="param-savelog"/>
0
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57 </inputs>
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58 <outputs>
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59 <expand macro="logfile-output"/>
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60 <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
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61 <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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66 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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67 <output name="summary">
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68 <assert_contents>
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69 <has_text text="forest-pasture"/>
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70 <has_text text="pasture-forest"/>
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71 </assert_contents>
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72 </output>
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73 <output name="coverage">
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74 <assert_contents>
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75 <has_text text="dist"/>
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76 <has_text text="forest-pasture"/>
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77 <has_text text="pasture-forest"/>
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78 </assert_contents>
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79 </output>
2
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80 <param name="savelog" value="true"/>
0
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81 <expand macro="logfile-test"/>
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82 </test>
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83 <test>
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84 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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85 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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86 <param name="groups" value="forest,pasture"/>
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87 <param name="form2" value="discrete"/>
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88 <param name="step" value="0.25"/>
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89 <param name="cutoff" value="0.25"/>
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90 <output name="summary">
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91 <assert_contents>
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92 <has_text text="forest-pasture"/>
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93 <has_text text="pasture-forest"/>
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94 </assert_contents>
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95 </output>
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96 <output name="coverage">
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97 <assert_contents>
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98 <has_text text="dist"/>
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99 <has_text text="forest-pasture"/>
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100 <has_text text="pasture-forest"/>
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101 </assert_contents>
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102 </output>
2
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103 <param name="savelog" value="true"/>
0
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104 <expand macro="logfile-test"/>
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105 </test>
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106 </tests>
2
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107 <help><![CDATA[
0
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108
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109 @MOTHUR_OVERVIEW@
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110
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111
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112 **Command Documentation**
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113
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114 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.
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115
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116 .. _libshuff: https://www.mothur.org/wiki/Libshuff
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117
2
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118 ]]></help>
5
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119 <expand macro="citations">
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120 <citation type="doi">10.1128/AEM.67.9.4374-4376.2001</citation>
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121 <citation type="doi">10.1128/AEM.70.9.5485-5492.2004</citation>
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122 </expand>
0
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123 </tool>