annotate cooccurrence.xml @ 1:f83d1ed69978 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:12:25 -0400
parents 6cb0335df5db
children c2cf32e92e83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6cb0335df5db 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_cooccurrence" name="Cooccurrence" version="@WRAPPER_VERSION@.0">
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>tests whether presence-absence patterns differ from chance</description>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
6cb0335df5db 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"/>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$otu" otu.dat &&
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
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15 echo 'cooccurrence(
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 shared=otu.dat,
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17 metric=$metric,
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18 matrixmodel=$matrixmodel,
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 iters=$iters
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 #if $label:
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 ,label=${ str($label).replace(",","-") }
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #end if
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23 #if $groups:
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24 ,groups=${ str($groups).replace(",","-") }
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 #end if
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 )'
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 | sed 's/ //g' ## mothur trips over whitespace
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 | mothur
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 | tee mothur.out.log
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 ]]></command>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <inputs>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <param name="metric" type="select" label="metric - test metric for scoring">
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35 <option value="cscore" selected="true">cscore - species segregation</option>
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36 <option value="checker">checker - species segregation</option>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <option value="combo">combo - unique species pairs</option>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <option value="vratio">vratio - variance</option>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 </param>
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40 <param name="matrixmodel" type="select" label="matrixmodel - the scoring matrix" help="See the notes below on choosing a metric/matrixmodel combination">
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <option value="sim1">sim1</option>
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42 <option value="sim2" selected="true">sim2</option>
6cb0335df5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="sim3">sim3</option>
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44 <option value="sim4">sim4</option>
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45 <option value="sim5">sim5</option>
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46 <option value="sim6">sim6</option>
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47 <option value="sim7">sim7</option>
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48 <option value="sim8">sim8</option>
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49 <option value="sim9">sim9</option>
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50 </param>
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51 <param name="groups" type="select" optional="true" label="groups - Groups to include" multiple="true" help="By default all are included if no selection is made.">
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52 <options>
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53 <filter type="data_meta" ref="otu" key="groups"/>
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54 </options>
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55 </param>
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56 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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57 <expand macro="labeloptions"/>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <expand macro="logfile-output"/>
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62 <data name="out_summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: cooccurence.summary"/>
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63 </outputs>
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64 <tests>
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65 <test><!-- test with defaults -->
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66 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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67 <output name="out_summary" ftype="tabular">
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68 <assert_contents>
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69 <has_text text="zScore"/>
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70 <has_text text="cscore"/>
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71 <has_text text="unique"/>
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72 <has_text text="0.05"/>
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73 </assert_contents>
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74 </output>
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75 <expand macro="logfile-test"/>
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76 </test>
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77 <test><!-- test with label and group select -->
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78 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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79 <param name="metric" value="vratio"/>
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80 <param name="label" value="0.05,0.22,0.41"/>
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81 <param name="groups" value="forest,pasture"/>
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82 <output name="out_summary" ftype="tabular">
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83 <assert_contents>
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84 <has_text text="zScore"/>
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85 <has_text text="vratio"/>
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86 <not_has_text text="unique"/>
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87 <has_text text="0.05"/>
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88 </assert_contents>
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89 </output>
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90 <expand macro="logfile-test"/>
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91 </test>
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92 </tests>
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93 <help>
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94 <![CDATA[
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95
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96 @MOTHUR_OVERVIEW@
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97
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98 **Command Documentation**
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99
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100 The cooccurrence_ command variance calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance. The input is a shared_ file. The output can be filtered by groups and labels.
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101
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102
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103
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104 **metric**
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105
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106 The metric parameter options are **cscore**, **checker**, **combo** and **vratio**. Default=cscore. The cscore or checkerboard score [1] is a metric that measures species segregation. It is the mean number of checkerboard units per species pair. The checker metric [2] counts the number of species pairs forming a perfect checkerboard. The combo metric [3] is the number of unique species pairs. The vratio or variance ratio [4] is a measure of the species association calculated by the ratio of the variance in total species number to the sum of the variances of the species. ::
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107
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108 [1] Stone, L., and A. Roberts. 1990. The checkerboard score and species distributions. Ocelogia. 85:74-79.
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109 [2] Diamond, J. M. 1975. Assembly of species communities. Pages 342-444 in M. L. Cody and J. M. Diamond, editors. Ecology and evolution of communities. Harvard University Press, Cambridge, Massachusetts, USA.
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110 [3] Pielou, D. P., and E. C. Pielou. 1968 Association among species of infrequent occurrence: the insect and spider fauna of Polypours betulinus (Bulliard) Fries. Journal of Theoretical Biology 21:202-216.
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111 [4] Schluter, D. 1984. A variance test for detecting species associations, with some example applications. Ecology 65:998-1005.
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112 [5] Gotelli, Nicholas J. 2000. NULL MODEL ANALYSIS OF SPECIES CO-OCCURRENCE PATTERNS. Ecology 81:2606-2621.
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113
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114
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115
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116 **matrixmodel**
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117
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118 The matrixmodel parameter allows you to select the model you would like to use. Options are sim1, sim2, sim3, sim4, sim5, sim6, sim7, sim8 and sim9. Default=sim2.
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119
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120 Each sim implements a different algorithm for generating null matrices with constraints on the rows (species) and columns (sites).::
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121 ===================== ====================== ======================= ======================
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122 Rows Columns equiprobable Columns proportional Column totals fixed
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123 ===================== ====================== ======================= ======================
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124 Rows equiprobable sim1 sim6 sim3
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125 Rows proportional sim7 sim8 sim5
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126 Row totals fixed sim2 sim4 sim9
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127 ===================== ====================== ======================= ======================
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128
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129 Equiprobable rows or columns means that each row, column or both is not dependent on the original co-occurrence matrix. Each species or site has an equal change of occurring in the null matrix.
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130 Proportional rows or columns means that the proportion of occurrences in rows, columns or both in the original co-occurrence matrix are preserved but the totals may differ. Each species or site's chances of occurring are proportional to their occurrence in the original co-occurrence matrix.
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131 Fixed row or column totals preserves the total number of occurrences in rows, columns or both in the original co-occurrence matrix. Sim9 is a special case that is not probabilistic. Since both the row and column totals are preserved the only way to randomize the matrix is with a checkerboard swap. When a checkerboard appears in the matrix the 1s and 0s are swapped to their mirror image to preserve the species and site totals.
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132
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133 Checkerboard::
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134
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135 10
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136 01
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137
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138 Swap::
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139
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140 01
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141 10
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142
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143
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144 suggested metric/matrixmodel combinations::
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145 ======== ======== ======== ========
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146 cscore checker combo vratio
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147 ======== ======== ======== ========
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148 sim9 sim9 sim9 sim2
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149 sim2 sim2 sim2 sim4
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150 - - sim4 sim8
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151 - - sim8 -
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152 ======== ======== ======== ========
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153
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154
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155 Careful readers will note that none of the suggested matrixmodels have equiprobable rows (species). This is because tests of co-occurrence are quite sensitive to the frequency of species occurrence. As such, rowtotals should be maintained or at least kept proportional in the null models. Sim9 is well suited to co-occurrence matrices that have an "island list" structure. Island lists are often found in classical ecology datasets that contain species with well defined habitat patches and are rarely degenerate (matrices that contain empty rows or columns). Sim2 is well suited for co-occurrence matrices that have a "sample list" structure. Sample list structured data are found where species have relatively homogeneous habitats and degenerate matrices are not uncommon. In these matrices species will often occur in only one site.
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156 The default values of cscore and sim2 have been selected because the c-score is not very sensitive to noise in the data and when used with sim9 or sim2 is not particularly prone to false positives. Sim2 has been chosen because of the prevalence of degenerate matrices. These are just guidelines, however, be sure to select a metric and matrix model that is best suited to the type of data you are analyzing.
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157 It should be noted that sim9 cannot be used with vratio because in sim9 both the column and row totals are maintained, hence there will be no variance.
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158 Please see [5] for more details on metric/null model selection.
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159
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160
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161 .. _shared: https://www.mothur.org/wiki/Shared_file
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162 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
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163
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164 v1.26.0: Updated to Mothur 1.33
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165 ]]>
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166 </help>
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167 <expand macro="citations"/>
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168 </tool>