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comparison usher.xml @ 2:8f6c7638eab2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
author iuc
date Sun, 19 Dec 2021 15:53:23 +0000
parents 335665e15630
children 746b434c8fbb
comparison
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1:335665e15630 2:8f6c7638eab2
99 </data> 99 </data>
100 <data name="clades" format="txt" from_work_dir="clades.txt" label="${tool.name} on ${on_string}: clades"> 100 <data name="clades" format="txt" from_work_dir="clades.txt" label="${tool.name} on ${on_string}: clades">
101 <filter>output_options['save_mutation_annotated_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter> 101 <filter>output_options['save_mutation_annotated_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter>
102 </data> 102 </data>
103 <collection name='subtrees' type='list' label='${tool.name} on ${on_string}: subtrees'> 103 <collection name='subtrees' type='list' label='${tool.name} on ${on_string}: subtrees'>
104 <discover_datasets pattern='__designation_and_ext__' format="newick" directory='out_subtrees'/> 104 <discover_datasets pattern='(?P&lt;designation&gt;.*)\.nh' format="newick" directory='out_subtrees'/>
105 <filter>output_options['write_subtrees_size']</filter> 105 <filter>output_options['write_subtrees_size']</filter>
106 </collection> 106 </collection>
107 <collection name='subtrees_expanded' type='list' label='${tool.name} on ${on_string}: subtrees expanded'> 107 <collection name='subtrees_expanded' type='list' label='${tool.name} on ${on_string}: subtrees expanded'>
108 <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_expanded'/> 108 <discover_datasets pattern='(?P&lt;designation&gt;.*)\.txt' format='txt' directory='out_subtrees_expanded'/>
109 <filter>output_options['write_subtrees_size']</filter> 109 <filter>output_options['write_subtrees_size']</filter>
110 </collection> 110 </collection>
111 <collection name='subtrees_mutations' type='list' label='${tool.name} on ${on_string}: subtrees mutations'> 111 <collection name='subtrees_mutations' type='list' label='${tool.name} on ${on_string}: subtrees mutations'>
112 <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_mutations'/> 112 <discover_datasets pattern='(?P&lt;designation&gt;.*)\.txt' format='txt' directory='out_subtrees_mutations'/>
113 <filter>output_options['write_subtrees_size']</filter> 113 <filter>output_options['write_subtrees_size']</filter>
114 </collection> 114 </collection>
115 <data name="current_tree" format="newick" from_work_dir="current-tree.nh" label="${tool.name} on ${on_string}: current tree"> 115 <data name="current_tree" format="newick" from_work_dir="current-tree.nh" label="${tool.name} on ${on_string}: current tree">
116 <filter>output_options['write_parsimony_scores_per_node'] is True</filter> 116 <filter>output_options['write_parsimony_scores_per_node'] is True</filter>
117 </data> 117 </data>
129 </data> 129 </data>
130 </outputs> 130 </outputs>
131 <tests> 131 <tests>
132 <test expect_num_outputs="3"> 132 <test expect_num_outputs="3">
133 <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" /> 133 <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" />
134 <param name="tree" value="global_phylo.nh"/> 134 <param name="tree" value="global_phylo.nh" ftype="newick"/>
135 <section name="collapse_options"> 135 <section name="collapse_options">
136 <param name="collapse_tree" value="true"/> 136 <param name="collapse_tree" value="true"/>
137 </section> 137 </section>
138 <section name="output_options"> 138 <section name="output_options">
139 <param name="save_mutation_annotated_tree" value="true"/> 139 <param name="save_mutation_annotated_tree" value="true" ftype="newick"/>
140 </section> 140 </section>
141 <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3"> 141 <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3">
142 <assert_contents> 142 <assert_contents>
143 <has_size value="26100" delta="100"/> 143 <has_size value="26100" delta="100"/>
144 </assert_contents> 144 </assert_contents>
146 <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/> 146 <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/>
147 <output name="final_tree" file="test_01_final_tree.nh" ftype="newick"/> 147 <output name="final_tree" file="test_01_final_tree.nh" ftype="newick"/>
148 </test> 148 </test>
149 <test expect_num_outputs="3"> 149 <test expect_num_outputs="3">
150 <param name="vcf" value="new_samples.vcf.gz"/> 150 <param name="vcf" value="new_samples.vcf.gz"/>
151 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 151 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
152 <section name="output_options"> 152 <section name="output_options">
153 <param name="write_uncondensed_final_tree" value="true"/> 153 <param name="write_uncondensed_final_tree" value="true"/>
154 </section> 154 </section>
155 <output name="uncondensed_tree" file="test_02_uncondensed_tree.nh" ftype="newick"/> 155 <output name="uncondensed_tree" file="test_02_uncondensed_tree.nh" ftype="newick"/>
156 <output name="mutation_paths" file="test_02_mutation_path.nh" ftype="txt"/> 156 <output name="mutation_paths" file="test_02_mutation_path.nh" ftype="txt"/>
160 </assert_contents> 160 </assert_contents>
161 </output> 161 </output>
162 </test> 162 </test>
163 <test expect_num_outputs="4"> 163 <test expect_num_outputs="4">
164 <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" /> 164 <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" />
165 <param name="tree" value="global_phylo.nh"/> 165 <param name="tree" value="global_phylo.nh" ftype="newick"/>
166 <param name="sort_mode" value="--sort-before-placement-1"/> 166 <param name="sort_mode" value="--sort-before-placement-1"/>
167 <section name="collapse_options"> 167 <section name="collapse_options">
168 <param name="collapse_tree" value="true"/> 168 <param name="collapse_tree" value="true"/>
169 </section> 169 </section>
170 <output name="condensed_tree" file="test_03_condensed_tree.nh" ftype="newick"/> 170 <output name="condensed_tree" file="test_03_condensed_tree.nh" ftype="newick"/>
180 </assert_contents> 180 </assert_contents>
181 </output> 181 </output>
182 </test> 182 </test>
183 <test expect_num_outputs="6"> 183 <test expect_num_outputs="6">
184 <param name="vcf" value="new_samples.vcf.gz"/> 184 <param name="vcf" value="new_samples.vcf.gz"/>
185 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 185 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
186 <section name="output_options"> 186 <section name="output_options">
187 <param name="write_uncondensed_final_tree" value="true"/> 187 <param name="write_uncondensed_final_tree" value="true"/>
188 <param name="write_subtrees_size" value="20"/> 188 <param name="write_subtrees_size" value="20"/>
189 </section> 189 </section>
190 <output name="uncondensed_tree" file="test_04_uncondensed_tree.nh" ftype="newick"/> 190 <output name="uncondensed_tree" file="test_04_uncondensed_tree.nh" ftype="newick"/>
204 <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/> 204 <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/>
205 </output_collection> 205 </output_collection>
206 </test> 206 </test>
207 <test expect_num_outputs="2"> 207 <test expect_num_outputs="2">
208 <param name="vcf" value="new_samples.vcf.gz"/> 208 <param name="vcf" value="new_samples.vcf.gz"/>
209 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 209 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
210 <section name="output_options"> 210 <section name="output_options">
211 <param name="write_parsimony_scores_per_node" value="true"/> 211 <param name="write_parsimony_scores_per_node" value="true"/>
212 </section> 212 </section>
213 <output name="current_tree" file="test_05_current_tree.nw" ftype="newick"/> 213 <output name="current_tree" file="test_05_current_tree.nw" ftype="newick"/>
214 <output name="parsimony_scores" file="test_05_parsimony_scores.tabular" ftype="tabular"/> 214 <output name="parsimony_scores" file="test_05_parsimony_scores.tabular" ftype="tabular"/>
215 </test> 215 </test>
216 <test expect_num_outputs="3"> 216 <test expect_num_outputs="3">
217 <param name="vcf" value="new_samples.vcf.gz"/> 217 <param name="vcf" value="new_samples.vcf.gz"/>
218 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 218 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
219 <section name="output_options"> 219 <section name="output_options">
220 <param name="multiple_placements" value="2"/> 220 <param name="multiple_placements" value="2"/>
221 </section> 221 </section>
222 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/> 222 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/>
223 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/> 223 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/>
227 </assert_contents> 227 </assert_contents>
228 </output> 228 </output>
229 </test> 229 </test>
230 <test expect_num_outputs="6"> 230 <test expect_num_outputs="6">
231 <param name="vcf" value="new_samples.vcf.gz"/> 231 <param name="vcf" value="new_samples.vcf.gz"/>
232 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 232 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
233 <section name="output_options"> 233 <section name="output_options">
234 <param name="write_single_subtree" value="2"/> 234 <param name="write_single_subtree" value="2"/>
235 </section> 235 </section>
236 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/> 236 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/>
237 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/> 237 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/>
248 </assert_contents> 248 </assert_contents>
249 </output> 249 </output>
250 </test> 250 </test>
251 <test expect_num_outputs="3"> 251 <test expect_num_outputs="3">
252 <param name="vcf" value="new_samples.vcf.gz"/> 252 <param name="vcf" value="new_samples.vcf.gz"/>
253 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 253 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
254 <param name="sort_mode" value="--sort-before-placement-2"/> 254 <param name="sort_mode" value="--sort-before-placement-2"/>
255 <output name="final_tree" file="test_08_final_tree.nh" ftype="newick"/> 255 <output name="final_tree" file="test_08_final_tree.nh" ftype="newick"/>
256 <output name="mutation_paths" file="test_08_mutation_path.nh" ftype="txt"/> 256 <output name="mutation_paths" file="test_08_mutation_path.nh" ftype="txt"/>
257 <output name="clades" ftype="txt"> 257 <output name="clades" ftype="txt">
258 <assert_contents> 258 <assert_contents>
260 </assert_contents> 260 </assert_contents>
261 </output> 261 </output>
262 </test> 262 </test>
263 <test expect_num_outputs="3"> 263 <test expect_num_outputs="3">
264 <param name="vcf" value="new_samples.vcf.gz"/> 264 <param name="vcf" value="new_samples.vcf.gz"/>
265 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 265 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
266 <param name="sort_mode" value="--sort-before-placement-3"/> 266 <param name="sort_mode" value="--sort-before-placement-3"/>
267 <output name="final_tree" file="test_09_final_tree.nh" ftype="newick"/> 267 <output name="final_tree" file="test_09_final_tree.nh" ftype="newick"/>
268 <output name="mutation_paths" file="test_09_mutation_path.nh" ftype="txt"/> 268 <output name="mutation_paths" file="test_09_mutation_path.nh" ftype="txt"/>
269 <output name="clades" ftype="txt"> 269 <output name="clades" ftype="txt">
270 <assert_contents> 270 <assert_contents>
272 </assert_contents> 272 </assert_contents>
273 </output> 273 </output>
274 </test> 274 </test>
275 <test expect_num_outputs="3"> 275 <test expect_num_outputs="3">
276 <param name="vcf" value="new_samples.vcf.gz"/> 276 <param name="vcf" value="new_samples.vcf.gz"/>
277 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 277 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
278 <param name="sort_mode" value="--sort-before-placement-1 --reverse-sort"/> 278 <param name="sort_mode" value="--sort-before-placement-1 --reverse-sort"/>
279 <output name="final_tree" file="test_10_final_tree.nh" ftype="newick"/> 279 <output name="final_tree" file="test_10_final_tree.nh" ftype="newick"/>
280 <output name="mutation_paths" file="test_10_mutation_path.nh" ftype="txt"/> 280 <output name="mutation_paths" file="test_10_mutation_path.nh" ftype="txt"/>
281 <output name="clades" ftype="txt"> 281 <output name="clades" ftype="txt">
282 <assert_contents> 282 <assert_contents>
284 </assert_contents> 284 </assert_contents>
285 </output> 285 </output>
286 </test> 286 </test>
287 <test expect_num_outputs="3"> 287 <test expect_num_outputs="3">
288 <param name="vcf" value="new_samples.vcf.gz"/> 288 <param name="vcf" value="new_samples.vcf.gz"/>
289 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 289 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
290 <param name="sort_mode" value="--sort-before-placement-2 --reverse-sort"/> 290 <param name="sort_mode" value="--sort-before-placement-2 --reverse-sort"/>
291 <output name="final_tree" file="test_11_final_tree.nh" ftype="newick"/> 291 <output name="final_tree" file="test_11_final_tree.nh" ftype="newick"/>
292 <output name="mutation_paths" file="test_11_mutation_path.nh" ftype="txt"/> 292 <output name="mutation_paths" file="test_11_mutation_path.nh" ftype="txt"/>
293 <output name="clades" ftype="txt"> 293 <output name="clades" ftype="txt">
294 <assert_contents> 294 <assert_contents>
296 </assert_contents> 296 </assert_contents>
297 </output> 297 </output>
298 </test> 298 </test>
299 <test expect_num_outputs="3"> 299 <test expect_num_outputs="3">
300 <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/> 300 <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
301 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/> 301 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
302 <param name="retain_input_branch" value="true"/> 302 <param name="retain_input_branch" value="true"/>
303 <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/> 303 <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
304 <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/> 304 <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
305 <output name="clades" ftype="txt"> 305 <output name="clades" ftype="txt">
306 <assert_contents> 306 <assert_contents>