Mercurial > repos > ecology > estimate_endem

annotate EstimEndem.xml @ 0:f7a55ccf2a3e draft

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author ecology
date Tue, 20 May 2025 09:52:29 +0000
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children f3a977826375
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f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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1 <tool id="estimate_endem" name="EstimEndem" version="0.1.0+galaxy0" profile="21.05">
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2 <description>
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3 of each cell of a spatial grid
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4 </description>
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5
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6 <macros>
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7 <token name="@TOOL_VERSION@">1.0</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 </macros>
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10
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11 <requirements>
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12 <requirement type="package" version="1.0.8">r-phyloregion</requirement>
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13 <requirement type="package" version="1.6.5">r-matrix</requirement>
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14 <requirement type="package" version="5.8_1">r-ape</requirement>
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15 <requirement type="package" version="1.2.2">bioconductor-sparsearray</requirement>
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16 <requirement type="package" version="1.0_20">r-sf</requirement>
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17 <requirement type="package" version="2.2_0">r-sp</requirement>
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18 <requirement type="package" version="3.6_32">r-raster</requirement>
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19 <requirement type="package" version="1.1.4">r-dplyr</requirement>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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20 </requirements>
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22 <required_files>
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23 <include path="EstimEndem.R" />
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24 </required_files>
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25
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27 <command detect_errors="exit_code">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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28 <![CDATA[
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29 mkdir '$shapefile.extra_files_path' &&
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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30 Rscript '$__tool_directory__/EstimEndem.R'
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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31 '$phylogeny'
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32 '$occupancy'
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33 ${os.path.join( $coordinates_file_input.extra_files_path, "shapefile.shp" )}
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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34 '$nb_cluster'
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35 '$clustering_method'
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36
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37 &&
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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38 mv output.* '${shapefile.extra_files_path}'
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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39
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40 ]]>
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41 </command>
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42
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43 <inputs>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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44 <param name="phylogeny" type="data" format="newick" label="Phylogeny file (Newick format)" />
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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45 <param name="occupancy" type="data" format="tabular" label="Occupancy data (Tabular format)" />
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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46 <param name ="coordinates_file_input" type="data" format="shp" label="input_shapefile" help="Provide coordinates files"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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47 <param name="nb_cluster" type="integer" value="10" label="the number of cluster" help="choose the number of phyloregion"/>
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48 <param name ="clustering_method" type="select" checked="true"
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49 label="Choose a clustering method" help="choose">
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50 <option value="ward.D" selected="true">ward.D</option>
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51 <option value="ward.D2">ward.D2</option>
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52 <option value="single">single</option>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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53 <option value="complete">complete</option>
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54 <option value="average">UPGMA</option>
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55 <option value="mcquitty">WPGMA</option>
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56 <option value="median">WPGMC</option>
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57 <option value="centroid">UPGMC</option>
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58 </param>
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59
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60 </inputs>
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61 <outputs>
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62 <data name="shapefile" format="shp" label="shapefile"/>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="phylogeny" value="tree_file"/>
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68 <param name="occupancy" value="matrix_file"/>
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69 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
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70 <composite_data value="composite_dataset/shapefile.shp"/>
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71 <composite_data value="composite_dataset/shapefile.shx"/>
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72 <composite_data value="composite_dataset/shapefile.dbf"/>
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73 <composite_data value="composite_dataset/shapefile.prj"/>
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74 </param>
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75 <param name="nb_cluster" value="8"/>
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76 <param name="clustering_method" value="ward.D"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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77
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78 <output file="shapefile_out_1/shapefile_shp_test1.html" name="shapefile">
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79 <extra_files type="file" name="output.shp" value="shapefile_out_1/output.shp"/>
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80 <extra_files type="file" name="output.shx" value="shapefile_out_1/output.shx"/>
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81 <extra_files type="file" name="output.dbf" value="shapefile_out_1/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
82 <extra_files type="file" name="output.prj" value="shapefile_out_1/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
83 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
84 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
85
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
86 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
87 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
88 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
89 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
90 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
91 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
92 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
93 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
94 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
95 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
96 <param name="clustering_method" value="ward.D2"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
97
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
98 <output file="shapefile_out_2/shapefile_shp_test2.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
99 <extra_files type="file" name="output.shp" value="shapefile_out_2/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
100 <extra_files type="file" name="output.shx" value="shapefile_out_2/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
101 <extra_files type="file" name="output.dbf" value="shapefile_out_2/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
102 <extra_files type="file" name="output.prj" value="shapefile_out_2/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
103 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
104 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
105
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
106 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
107 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
108 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
109 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
110 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
111 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
112 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
113 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
114 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
115 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
116 <param name="clustering_method" value="single"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
117
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
118 <output file="shapefile_out_3/shapefile_shp_test3.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
119 <extra_files type="file" name="output.shp" value="shapefile_out_3/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
120 <extra_files type="file" name="output.shx" value="shapefile_out_3/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
121 <extra_files type="file" name="output.dbf" value="shapefile_out_3/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
122 <extra_files type="file" name="output.prj" value="shapefile_out_3/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
123 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
124 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
125
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
126 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
127 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
128 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
129 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
130 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
131 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
132 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
133 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
134 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
135 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
136 <param name="clustering_method" value="complete"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
137
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
138 <output file="shapefile_out_4/shapefile_shp_test4.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
139 <extra_files type="file" name="output.shp" value="shapefile_out_4/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
140 <extra_files type="file" name="output.shx" value="shapefile_out_4/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
141 <extra_files type="file" name="output.dbf" value="shapefile_out_4/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
142 <extra_files type="file" name="output.prj" value="shapefile_out_4/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
143 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
144 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
145
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
146 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
147 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
148 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
149 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
150 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
151 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
152 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
153 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
154 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
155 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
156 <param name="clustering_method" value="average"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
157
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
158 <output file="shapefile_out_5/shapefile_shp_test5.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
159 <extra_files type="file" name="output.shp" value="shapefile_out_5/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
160 <extra_files type="file" name="output.shx" value="shapefile_out_5/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
161 <extra_files type="file" name="output.dbf" value="shapefile_out_5/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
162 <extra_files type="file" name="output.prj" value="shapefile_out_5/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
163 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
164 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
165
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
166 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
167 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
168 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
169 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
170 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
171 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
172 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
173 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
174 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
175 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
176 <param name="clustering_method" value="mcquitty"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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177
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
178 <output file="shapefile_out_6/shapefile_shp_test6.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
179 <extra_files type="file" name="output.shp" value="shapefile_out_6/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
180 <extra_files type="file" name="output.shx" value="shapefile_out_6/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
181 <extra_files type="file" name="output.dbf" value="shapefile_out_6/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
182 <extra_files type="file" name="output.prj" value="shapefile_out_6/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
183 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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184 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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185
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
186 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
187 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
188 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
189 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
190 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
191 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
192 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
193 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
194 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
195 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
196 <param name="clustering_method" value="median"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
197
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
198 <output file="shapefile_out_7/shapefile_shp_test7.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
199 <extra_files type="file" name="output.shp" value="shapefile_out_7/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
200 <extra_files type="file" name="output.shx" value="shapefile_out_7/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
201 <extra_files type="file" name="output.dbf" value="shapefile_out_7/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
202 <extra_files type="file" name="output.prj" value="shapefile_out_7/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
203 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
204 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
205
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
206 <test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
207 <param name="phylogeny" value="tree_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
208 <param name="occupancy" value="matrix_file"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
209 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
210 <composite_data value="composite_dataset/shapefile.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
211 <composite_data value="composite_dataset/shapefile.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
212 <composite_data value="composite_dataset/shapefile.dbf"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
213 <composite_data value="composite_dataset/shapefile.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
214 </param>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
215 <param name="nb_cluster" value="8"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
216 <param name="clustering_method" value="centroid"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
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217
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
218 <output file="shapefile_out_8/shapefile_shp_test8.html" name="shapefile">
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
219 <extra_files type="file" name="output.shp" value="shapefile_out_8/output.shp"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
220 <extra_files type="file" name="output.shx" value="shapefile_out_8/output.shx"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
221 <extra_files type="file" name="output.dbf" value="shapefile_out_8/output.dbf" compare="sim_size" delta="50"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
222 <extra_files type="file" name="output.prj" value="shapefile_out_8/output.prj"/>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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diff changeset
223 </output>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
224 </test>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
225 </tests>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
226
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
227 <help>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
228 <![CDATA[
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
229 This tool estimates the endemism of each cell in a spatial grid using the provided phylogeny, occupancy data, and spatial coordinates.
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
230 Ensure that the input files are in the correct formats: Newick for phylogeny, tabular for occupancy, and shapefile for spatial data.
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
231
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
232 ]]>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
233 </help>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
234
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
235 <citations>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
236 <citation type="doi">10.32614/CRAN.package.phyloregion</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
237 <citation type="doi">10.32614/CRAN.package.Matrix</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
238 <citation type="doi">10.32614/CRAN.package.ape</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
239 <citation type="doi">10.18129/B9.bioc.SparseArray</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
240 <citation type="doi">10.32614/CRAN.package.sf</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
parents:
diff changeset
241 <citation type="doi">10.32614/CRAN.package.sp</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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243 <citation type="doi">10.32614/CRAN.package.dplyr</citation>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
ecology
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244 </citations>
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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245
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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246 </tool>