Mercurial > repos > ecology > estimate_endem

comparison EstimEndem.xml @ 0:f7a55ccf2a3e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
author ecology
date Tue, 20 May 2025 09:52:29 +0000
parents
children f3a977826375
comparison
equal deleted inserted replaced
-1:000000000000 0:f7a55ccf2a3e
1 <tool id="estimate_endem" name="EstimEndem" version="0.1.0+galaxy0" profile="21.05">
2 <description>
3 of each cell of a spatial grid
4 </description>
5
6 <macros>
7 <token name="@TOOL_VERSION@">1.0</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 </macros>
10
11 <requirements>
12 <requirement type="package" version="1.0.8">r-phyloregion</requirement>
13 <requirement type="package" version="1.6.5">r-matrix</requirement>
14 <requirement type="package" version="5.8_1">r-ape</requirement>
15 <requirement type="package" version="1.2.2">bioconductor-sparsearray</requirement>
16 <requirement type="package" version="1.0_20">r-sf</requirement>
17 <requirement type="package" version="2.2_0">r-sp</requirement>
18 <requirement type="package" version="3.6_32">r-raster</requirement>
19 <requirement type="package" version="1.1.4">r-dplyr</requirement>
20 </requirements>
21
22 <required_files>
23 <include path="EstimEndem.R" />
24 </required_files>
25
26
27 <command detect_errors="exit_code">
28 <![CDATA[
29 mkdir '$shapefile.extra_files_path' &&
30 Rscript '$__tool_directory__/EstimEndem.R'
31 '$phylogeny'
32 '$occupancy'
33 ${os.path.join( $coordinates_file_input.extra_files_path, "shapefile.shp" )}
34 '$nb_cluster'
35 '$clustering_method'
36
37 &&
38 mv output.* '${shapefile.extra_files_path}'
39
40 ]]>
41 </command>
42
43 <inputs>
44 <param name="phylogeny" type="data" format="newick" label="Phylogeny file (Newick format)" />
45 <param name="occupancy" type="data" format="tabular" label="Occupancy data (Tabular format)" />
46 <param name ="coordinates_file_input" type="data" format="shp" label="input_shapefile" help="Provide coordinates files"/>
47 <param name="nb_cluster" type="integer" value="10" label="the number of cluster" help="choose the number of phyloregion"/>
48 <param name ="clustering_method" type="select" checked="true"
49 label="Choose a clustering method" help="choose">
50 <option value="ward.D" selected="true">ward.D</option>
51 <option value="ward.D2">ward.D2</option>
52 <option value="single">single</option>
53 <option value="complete">complete</option>
54 <option value="average">UPGMA</option>
55 <option value="mcquitty">WPGMA</option>
56 <option value="median">WPGMC</option>
57 <option value="centroid">UPGMC</option>
58 </param>
59
60 </inputs>
61 <outputs>
62 <data name="shapefile" format="shp" label="shapefile"/>
63 </outputs>
64
65 <tests>
66 <test>
67 <param name="phylogeny" value="tree_file"/>
68 <param name="occupancy" value="matrix_file"/>
69 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
70 <composite_data value="composite_dataset/shapefile.shp"/>
71 <composite_data value="composite_dataset/shapefile.shx"/>
72 <composite_data value="composite_dataset/shapefile.dbf"/>
73 <composite_data value="composite_dataset/shapefile.prj"/>
74 </param>
75 <param name="nb_cluster" value="8"/>
76 <param name="clustering_method" value="ward.D"/>
77
78 <output file="shapefile_out_1/shapefile_shp_test1.html" name="shapefile">
79 <extra_files type="file" name="output.shp" value="shapefile_out_1/output.shp"/>
80 <extra_files type="file" name="output.shx" value="shapefile_out_1/output.shx"/>
81 <extra_files type="file" name="output.dbf" value="shapefile_out_1/output.dbf" compare="sim_size" delta="50"/>
82 <extra_files type="file" name="output.prj" value="shapefile_out_1/output.prj"/>
83 </output>
84 </test>
85
86 <test>
87 <param name="phylogeny" value="tree_file"/>
88 <param name="occupancy" value="matrix_file"/>
89 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
90 <composite_data value="composite_dataset/shapefile.shp"/>
91 <composite_data value="composite_dataset/shapefile.shx"/>
92 <composite_data value="composite_dataset/shapefile.dbf"/>
93 <composite_data value="composite_dataset/shapefile.prj"/>
94 </param>
95 <param name="nb_cluster" value="8"/>
96 <param name="clustering_method" value="ward.D2"/>
97
98 <output file="shapefile_out_2/shapefile_shp_test2.html" name="shapefile">
99 <extra_files type="file" name="output.shp" value="shapefile_out_2/output.shp"/>
100 <extra_files type="file" name="output.shx" value="shapefile_out_2/output.shx"/>
101 <extra_files type="file" name="output.dbf" value="shapefile_out_2/output.dbf" compare="sim_size" delta="50"/>
102 <extra_files type="file" name="output.prj" value="shapefile_out_2/output.prj"/>
103 </output>
104 </test>
105
106 <test>
107 <param name="phylogeny" value="tree_file"/>
108 <param name="occupancy" value="matrix_file"/>
109 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
110 <composite_data value="composite_dataset/shapefile.shp"/>
111 <composite_data value="composite_dataset/shapefile.shx"/>
112 <composite_data value="composite_dataset/shapefile.dbf"/>
113 <composite_data value="composite_dataset/shapefile.prj"/>
114 </param>
115 <param name="nb_cluster" value="8"/>
116 <param name="clustering_method" value="single"/>
117
118 <output file="shapefile_out_3/shapefile_shp_test3.html" name="shapefile">
119 <extra_files type="file" name="output.shp" value="shapefile_out_3/output.shp"/>
120 <extra_files type="file" name="output.shx" value="shapefile_out_3/output.shx"/>
121 <extra_files type="file" name="output.dbf" value="shapefile_out_3/output.dbf" compare="sim_size" delta="50"/>
122 <extra_files type="file" name="output.prj" value="shapefile_out_3/output.prj"/>
123 </output>
124 </test>
125
126 <test>
127 <param name="phylogeny" value="tree_file"/>
128 <param name="occupancy" value="matrix_file"/>
129 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
130 <composite_data value="composite_dataset/shapefile.shp"/>
131 <composite_data value="composite_dataset/shapefile.shx"/>
132 <composite_data value="composite_dataset/shapefile.dbf"/>
133 <composite_data value="composite_dataset/shapefile.prj"/>
134 </param>
135 <param name="nb_cluster" value="8"/>
136 <param name="clustering_method" value="complete"/>
137
138 <output file="shapefile_out_4/shapefile_shp_test4.html" name="shapefile">
139 <extra_files type="file" name="output.shp" value="shapefile_out_4/output.shp"/>
140 <extra_files type="file" name="output.shx" value="shapefile_out_4/output.shx"/>
141 <extra_files type="file" name="output.dbf" value="shapefile_out_4/output.dbf" compare="sim_size" delta="50"/>
142 <extra_files type="file" name="output.prj" value="shapefile_out_4/output.prj"/>
143 </output>
144 </test>
145
146 <test>
147 <param name="phylogeny" value="tree_file"/>
148 <param name="occupancy" value="matrix_file"/>
149 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
150 <composite_data value="composite_dataset/shapefile.shp"/>
151 <composite_data value="composite_dataset/shapefile.shx"/>
152 <composite_data value="composite_dataset/shapefile.dbf"/>
153 <composite_data value="composite_dataset/shapefile.prj"/>
154 </param>
155 <param name="nb_cluster" value="8"/>
156 <param name="clustering_method" value="average"/>
157
158 <output file="shapefile_out_5/shapefile_shp_test5.html" name="shapefile">
159 <extra_files type="file" name="output.shp" value="shapefile_out_5/output.shp"/>
160 <extra_files type="file" name="output.shx" value="shapefile_out_5/output.shx"/>
161 <extra_files type="file" name="output.dbf" value="shapefile_out_5/output.dbf" compare="sim_size" delta="50"/>
162 <extra_files type="file" name="output.prj" value="shapefile_out_5/output.prj"/>
163 </output>
164 </test>
165
166 <test>
167 <param name="phylogeny" value="tree_file"/>
168 <param name="occupancy" value="matrix_file"/>
169 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
170 <composite_data value="composite_dataset/shapefile.shp"/>
171 <composite_data value="composite_dataset/shapefile.shx"/>
172 <composite_data value="composite_dataset/shapefile.dbf"/>
173 <composite_data value="composite_dataset/shapefile.prj"/>
174 </param>
175 <param name="nb_cluster" value="8"/>
176 <param name="clustering_method" value="mcquitty"/>
177
178 <output file="shapefile_out_6/shapefile_shp_test6.html" name="shapefile">
179 <extra_files type="file" name="output.shp" value="shapefile_out_6/output.shp"/>
180 <extra_files type="file" name="output.shx" value="shapefile_out_6/output.shx"/>
181 <extra_files type="file" name="output.dbf" value="shapefile_out_6/output.dbf" compare="sim_size" delta="50"/>
182 <extra_files type="file" name="output.prj" value="shapefile_out_6/output.prj"/>
183 </output>
184 </test>
185
186 <test>
187 <param name="phylogeny" value="tree_file"/>
188 <param name="occupancy" value="matrix_file"/>
189 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
190 <composite_data value="composite_dataset/shapefile.shp"/>
191 <composite_data value="composite_dataset/shapefile.shx"/>
192 <composite_data value="composite_dataset/shapefile.dbf"/>
193 <composite_data value="composite_dataset/shapefile.prj"/>
194 </param>
195 <param name="nb_cluster" value="8"/>
196 <param name="clustering_method" value="median"/>
197
198 <output file="shapefile_out_7/shapefile_shp_test7.html" name="shapefile">
199 <extra_files type="file" name="output.shp" value="shapefile_out_7/output.shp"/>
200 <extra_files type="file" name="output.shx" value="shapefile_out_7/output.shx"/>
201 <extra_files type="file" name="output.dbf" value="shapefile_out_7/output.dbf" compare="sim_size" delta="50"/>
202 <extra_files type="file" name="output.prj" value="shapefile_out_7/output.prj"/>
203 </output>
204 </test>
205
206 <test>
207 <param name="phylogeny" value="tree_file"/>
208 <param name="occupancy" value="matrix_file"/>
209 <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
210 <composite_data value="composite_dataset/shapefile.shp"/>
211 <composite_data value="composite_dataset/shapefile.shx"/>
212 <composite_data value="composite_dataset/shapefile.dbf"/>
213 <composite_data value="composite_dataset/shapefile.prj"/>
214 </param>
215 <param name="nb_cluster" value="8"/>
216 <param name="clustering_method" value="centroid"/>
217
218 <output file="shapefile_out_8/shapefile_shp_test8.html" name="shapefile">
219 <extra_files type="file" name="output.shp" value="shapefile_out_8/output.shp"/>
220 <extra_files type="file" name="output.shx" value="shapefile_out_8/output.shx"/>
221 <extra_files type="file" name="output.dbf" value="shapefile_out_8/output.dbf" compare="sim_size" delta="50"/>
222 <extra_files type="file" name="output.prj" value="shapefile_out_8/output.prj"/>
223 </output>
224 </test>
225 </tests>
226
227 <help>
228 <![CDATA[
229 This tool estimates the endemism of each cell in a spatial grid using the provided phylogeny, occupancy data, and spatial coordinates.
230 Ensure that the input files are in the correct formats: Newick for phylogeny, tabular for occupancy, and shapefile for spatial data.
231
232 ]]>
233 </help>
234
235 <citations>
236 <citation type="doi">10.32614/CRAN.package.phyloregion</citation>
237 <citation type="doi">10.32614/CRAN.package.Matrix</citation>
238 <citation type="doi">10.32614/CRAN.package.ape</citation>
239 <citation type="doi">10.18129/B9.bioc.SparseArray</citation>
240 <citation type="doi">10.32614/CRAN.package.sf</citation>
241 <citation type="doi">10.32614/CRAN.package.sp</citation>
242 <citation type="doi">10.32614/CRAN.package.raster</citation>
243 <citation type="doi">10.32614/CRAN.package.dplyr</citation>
244 </citations>
245
246 </tool>