Mercurial > repos > ecology > claraguess

annotate claraguess.xml @ 0:52d4151e00d8 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
author ecology
date Wed, 28 May 2025 10:12:06 +0000
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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1 <tool id="ClaraGuess" name="Clara Estimate and Clustering" version="0.1.2" profile="23.2">
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2 <description>Environmental clustering using CLARA and BRT predictions</description>
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3
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4 <requirements>
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5 <requirement type="package" version="4.3.3">r-base</requirement>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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6 <requirement type="package" version="2.1.8.1">r-cluster</requirement>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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8 <requirement type="package" version="2.0.0">r-tidyverse</requirement>
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9 </requirements>
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10
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript '$__tool_directory__/claraguess.R'
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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13 '$enviro'
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14 '$preds'
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15 '$taxas'
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16 '$type'
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17 '$k'
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18 '$metric'
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19 '$samples'
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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20 '$data_cluster'
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21 '$silhouette_plot'
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22 #if str($type) == "auto":
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23 '$sih_scores'
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24 #else:
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25 'NA'
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26 #end if
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27 '$clustered_taxas_env'
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28 ]]></command>
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29
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30 <inputs>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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31 <param name="enviro" type="data" format="tabular" label="Environmental data (tabular)"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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32 <param name="preds" type="data" format="tabular" multiple="true" label="BRT prediction files (collection of tabular)"/>
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33 <param name="taxas" type="data" format="txt" label="List of taxa (from TaxaSeeker)"/>
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34
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35 <param name="type" type="select" label="k is ...">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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36 <option value="fixed">the number of clusters (fixed)</option>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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37 <option value="auto">the maximum number of clusters (automatic)</option>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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38 </param>
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39
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40 <param name="k" type="integer" optional="true" label="Value of k"/>
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41
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42 <param name="metric" type="select" label=" dissimilarity metric">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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43 <option value="manhattan">Manhattan</option>
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44 <option value="jaccard">Jaccard</option>
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45 <option value="euclidean" selected="true">Euclidean</option>
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46 </param>
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47
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48 <param name="samples" type="integer" value="1000" label="Number of samples for CLARA"/>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="data_cluster" from_work_dir="data_cluster.tabular" format="tabular" label="Cluster assignments (lat, long, cluster)"/>
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53 <data name="silhouette_plot" from_work_dir="silhouette_plot.png" format="png" label="Silhouette Index Plot"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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54 <data name="sih_scores" from_work_dir="sih_scores.png" format="png" label="Silhouette Plot">
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55 <filter>type == "auto"</filter>
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56 </data>
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57 <data name="clustered_taxas_env" from_work_dir="clustered_taxas_env.tabular" format="tabular" label="Environment + Clustered Data"/>
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58 </outputs>
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59
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60 <tests>
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61 <test expect_num_outputs="3">
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62 <param name="enviro" value="enviro.tabular"/>
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63 <param name="preds" value="preds.tabular"/>
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64 <param name="taxas" value="taxas.tabular"/>
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65 <param name="type" value="fixed"/>
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66 <param name="k" value="3"/>
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67 <param name="metric" value="manhattan"/>
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68 <param name="samples" value="10"/>
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69
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70 <output name="data_cluster">
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71 <assert_contents>
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72 <has_line_matching expression="^lat\tlong\tcluster$"/>
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73 <has_n_columns n="3"/>
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74 </assert_contents>
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75 </output>
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76
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77 <output name="silhouette_plot">
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78 <assert_contents>
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79 <has_size value="8400" delta="600"/>
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80 </assert_contents>
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81 </output>
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82
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ecology
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83 <output name="clustered_taxas_env">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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84 <assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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85 <has_line_matching expression="^lat\tlong\tcluster.*$"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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86 </assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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87 </output>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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88 </test>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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89
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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90 <test expect_num_outputs="4">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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91 <param name="enviro" value="enviro.tabular"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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92 <param name="preds" value="preds.tabular"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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93 <param name="taxas" value="taxas.tabular"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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94 <param name="type" value="auto"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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95 <param name="k" value="3"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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96 <param name="metric" value="manhattan"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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97 <param name="samples" value="10"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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98
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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99 <output name="data_cluster">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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100 <assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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101 <has_line_matching expression="^lat\tlong\tcluster$"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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102 <has_n_columns n="3"/>
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103 </assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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104 </output>
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105
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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106 <output name="silhouette_plot">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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107 <assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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108 <has_size value="8400" delta="600"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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109 </assert_contents>
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110 </output>
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111
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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112 <output name="sih_scores">
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113 <assert_contents>
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114 <has_size value="6918" delta="600"/>
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115 </assert_contents>
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116 </output>
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117
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118 <output name="clustered_taxas_env">
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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119 <assert_contents>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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120 <has_line_matching expression="^lat\tlong\tcluster.*$"/>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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121 </assert_contents>
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122 </output>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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123 </test>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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124 </tests>
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125
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126 <help><![CDATA[
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127 ==================
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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128 **What it does ?**
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129 ==================
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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130
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131 This tool applies the CLARA clustering method to identify environmental clusters based on:
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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132 - BRT model predictions (a collection of tabular files),
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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133 - environmental variables (tabular),
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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134 - a list of taxa (tabular, from TaxaSeeker).
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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135 The tool enables the determination of the optimal number of clusters for partition-based clustering (if automatic mode is selected), along with generating files used in the subsequent ecoregionalization workflow.
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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136
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137 ===================
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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138 **How to use it ?**
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139 ===================
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140
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141 ## Parameters:
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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142
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143 - **Clustering type**: Choose between a fixed number of clusters ("Number of clusters") or an automatic mode using a maximum number ("Max number of clusters").
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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144 - **k**: The number of clusters (used based on the selected mode).
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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145 - **Distance metric**: dissimilarity metric / distance used in clustering (Manhattan, Jaccard, or Euclidean).
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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146 - **Samples**: Number of samples drawn for CLARA clustering.
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147
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148 ## Outputs:
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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149
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150 - A tabular file containing cluster assignments for each geographic point (columns: lat, long, cluster).
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151 - A collection of:
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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152 - A silhouette plot (PNG),
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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153 - A silhouette index plot (PNG),
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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154 - A tabular file with original environmental variables and predicted cluster number.
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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155
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156 This tool is useful for ecological modeling and spatial analysis, particularly in marine or terrestrial biogeography contexts.
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157
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158 **Example of the environemental file :**
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159
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160 +------+------+---------+------+--------------+-----+
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161 | long | lat | Carbo | Grav | Maxbearing | ... |
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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162 +------+------+---------+------+--------------+-----+
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163 |139.22|-65.57| 0.88 |28.59 | 3.67 | ... |
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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164 +------+------+---------+------+--------------+-----+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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165 |139.22|-65.57| 0.88 |28.61 | 3.64 | ... |
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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166 +------+------+---------+------+--------------+-----+
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167 | ... | ... | ... | ... | ... | ... |
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168 +------+------+---------+------+--------------+-----+
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169
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170 **Example of the Brt prediction file :**
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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171
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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172 +-----------+----------+-----------------------+-------------+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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173 | lat | long | Prediction.index | spe |
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174 +-----------+----------+-----------------------+-------------+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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175 | -65.57 | 139.22 | 0.122438487221909 | Acarnidae |
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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176 +-----------+----------+-----------------------+-------------+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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177 | -65.57 | 139.32 | 0.119154535627801 | Acarnidae |
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178 +-----------+----------+-----------------------+-------------+
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179 | ... | ... | ... | ... |
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180 +-----------+----------+-----------------------+-------------+
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181
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182 ]]></help>
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183
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184 <citations>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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185 <citation type="doi">10.32614/CRAN.package.dplyr</citation>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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186 <citation type="doi">10.32614/CRAN.package.cluster</citation>
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187 <citation type="doi">10.32614/CRAN.package.tidyverse</citation>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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188 </citations>
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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189 </tool>