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comparison busco.xml @ 20:9da899448a8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58
author iuc
date Tue, 29 Oct 2024 14:13:26 +0000
parents 1b5840963240
children c209d02621e7
comparison
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19:1b5840963240 20:9da899448a8a
1 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>Assess genome assembly and annotation completeness</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">busco</xref> 7 <xref type="bio.tools">busco</xref>
52 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot': 52 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
53 --miniprot 53 --miniprot
54 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus': 54 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
55 ${busco_mode.use_augustus.long} 55 ${busco_mode.use_augustus.long}
56 --augustus 56 --augustus
57
58 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin': 57 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
59 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}' 58 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': 59 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
61 --augustus_species local 60 --augustus_species local
62 #end if 61 #end if
82 ## gff files can be absent 81 ## gff files can be absent
83 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true 82 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
84 #end if 83 #end if
85 84
86 85
87 ]]> </command> 86 ]]></command>
88 <inputs> 87 <inputs>
89 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." /> 88 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."/>
90 <conditional name="lineage_conditional"> 89 <conditional name="lineage_conditional">
91 <param name="selector" type="select" label="Lineage data source"> 90 <param name="selector" type="select" label="Lineage data source">
92 <option value="download">Download lineage data</option> 91 <option value="download">Download lineage data</option>
93 <option value="cached">Use cached lineage data</option> 92 <option value="cached">Use cached lineage data</option>
94 </param> 93 </param>
95 <when value="cached"> 94 <when value="cached">
96 <param name="cached_db" label="Cached database with lineage" type="select"> 95 <param name="cached_db" label="Cached database with lineage" type="select">
97 <options from_data_table="busco_database"> 96 <options from_data_table="busco_database">
98 <validator message="No BUSCO database is available" type="no_options" /> 97 <validator message="No BUSCO database is available" type="no_options"/>
99 </options> 98 </options>
100 </param> 99 </param>
101 </when> 100 </when>
102 <when value="download"/> 101 <when value="download"/>
103 </conditional> 102 </conditional>
111 <conditional name="use_augustus"> 110 <conditional name="use_augustus">
112 <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor"> 111 <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
113 <option value="augustus">Augustus</option> 112 <option value="augustus">Augustus</option>
114 <option value="metaeuk">Metaeuk</option> 113 <option value="metaeuk">Metaeuk</option>
115 <option value="miniprot" selected="true">Miniprot</option> 114 <option value="miniprot" selected="true">Miniprot</option>
116
117 </param> 115 </param>
118 <when value="metaeuk"/> 116 <when value="metaeuk"/>
119 <when value="miniprot"/> 117 <when value="miniprot"/>
120 <when value="augustus"> 118 <when value="augustus">
121 <conditional name="aug_prediction"> 119 <conditional name="aug_prediction">
122 <param name="augustus_mode" type="select" label="Augustus species model"> 120 <param name="augustus_mode" type="select" label="Augustus species model">
123 <option value="no" selected="true">Use the default species for selected lineage</option> 121 <option value="no" selected="true">Use the default species for selected lineage</option>
124 <option value="builtin">Use another predefined species model</option> 122 <option value="builtin">Use another predefined species model</option>
125 <option value="history">Use a custom species model</option> 123 <option value="history">Use a custom species model</option>
126 </param> 124 </param>
127 <when value="no" /> 125 <when value="no"/>
128 <when value="history"> 126 <when value="history">
129 <param name="augustus_model" type="data" format="augustus" label="Augustus model" /> 127 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
130 </when> 128 </when>
131 <when value="builtin"> 129 <when value="builtin">
132 <param name="augustus_species" type="select" label="Augustus species model"> 130 <param name="augustus_species" type="select" label="Augustus species model">
133 <expand macro="augustus_species" /> 131 <expand macro="augustus_species"/>
134 </param> 132 </param>
135 </when> 133 </when>
136 </conditional> 134 </conditional>
137 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" /> 135 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
138 </when> 136 </when>
139 </conditional> 137 </conditional>
140 </when> 138 </when>
141 <when value="tran" /> 139 <when value="tran"/>
142 <when value="prot" /> 140 <when value="prot"/>
143 </conditional> 141 </conditional>
144
145 <conditional name="lineage"> 142 <conditional name="lineage">
146 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage"> 143 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
147 <option value="auto_detect">Auto-detect</option> 144 <option value="auto_detect">Auto-detect</option>
148 <option value="select_lineage">Select lineage</option> 145 <option value="select_lineage">Select lineage</option>
149 </param> 146 </param>
154 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option> 151 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
155 </param> 152 </param>
156 </when> 153 </when>
157 <when value="select_lineage"> 154 <when value="select_lineage">
158 <param argument="--lineage_dataset" type="select" label="Lineage"> 155 <param argument="--lineage_dataset" type="select" label="Lineage">
159 <expand macro="lineages" /> 156 <expand macro="lineages"/>
160 </param> 157 </param>
161 </when> 158 </when>
162 </conditional> 159 </conditional>
163 160
164 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 161 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
167 <option value="image">summary image</option> 164 <option value="image">summary image</option>
168 <option value="gff">gff</option> 165 <option value="gff">gff</option>
169 </param> 166 </param>
170 167
171 <section name="adv" title="Advanced Options" expanded="False"> 168 <section name="adv" title="Advanced Options" expanded="False">
172 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> 169 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/>
173 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> 170 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
174 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/> 171 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
175 </section> 172 </section>
176 </inputs> 173 </inputs>
177 174
178 <outputs> 175 <outputs>
179 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> 176 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
180 <filter>outputs and 'short_summary' in outputs</filter> 177 <filter>outputs and 'short_summary' in outputs</filter>
181 </data> 178 </data>
182 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> 179 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
183 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"> 180 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
184 <filter>outputs and 'missing' in outputs</filter> 181 <filter>outputs and 'missing' in outputs</filter>
185 </data> 182 </data>
186 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> 183 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
187 <filter>outputs and 'image' in outputs</filter> 184 <filter>outputs and 'image' in outputs</filter>
191 </data> 188 </data>
192 </outputs> 189 </outputs>
193 190
194 <tests> 191 <tests>
195 <test expect_num_outputs="4"> 192 <test expect_num_outputs="4">
196 <param name="input" value="genome.fa" /> 193 <param name="input" value="genome.fa"/>
197 <conditional name="lineage"> 194 <conditional name="lineage">
198 <param name="lineage_mode" value="select_lineage" /> 195 <param name="lineage_mode" value="select_lineage"/>
199 <param name="lineage_dataset" value="arthropoda_odb10" /> 196 <param name="lineage_dataset" value="arthropoda_odb10"/>
200 </conditional> 197 </conditional>
201 <conditional name="busco_mode"> 198 <conditional name="busco_mode">
202 <param name="mode" value="geno" /> 199 <param name="mode" value="geno"/>
203 <conditional name="use_augustus"> 200 <conditional name="use_augustus">
204 <param name="use_augustus_selector" value="augustus" /> 201 <param name="use_augustus_selector" value="augustus"/>
205 </conditional> 202 </conditional>
206 </conditional> 203 </conditional>
207 <param name="outputs" value="short_summary,missing,gff" /> 204 <param name="outputs" value="short_summary,missing,gff"/>
208 <output name="busco_sum"> 205 <output name="busco_sum">
209 <assert_contents> 206 <assert_contents>
210 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 207 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
211 <has_text text="Gene predictor used: augustus"/> 208 <has_text text="Gene predictor used: augustus"/>
212 </assert_contents> 209 </assert_contents>
213 </output> 210 </output>
214 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> 211 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
215 <output name="busco_gff"> 212 <output name="busco_gff">
216 <assert_contents> 213 <assert_contents>
217 <has_n_lines n="1"/> 214 <has_n_lines n="1"/>
218 <has_text text="##gff-version 3" /> 215 <has_text text="##gff-version 3"/>
219 </assert_contents> 216 </assert_contents>
220 </output> 217 </output>
221 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/> 218 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
222 </test> 219 </test>
223 <test expect_num_outputs="5"> 220 <test expect_num_outputs="5">
224 <param name="input" value="proteome.fa" /> 221 <param name="input" value="proteome.fa"/>
225 <conditional name="lineage"> 222 <conditional name="lineage">
226 <param name="lineage_mode" value="select_lineage" /> 223 <param name="lineage_mode" value="select_lineage"/>
227 <param name="lineage_dataset" value="arthropoda_odb10" /> 224 <param name="lineage_dataset" value="arthropoda_odb10"/>
228 </conditional> 225 </conditional>
229 <conditional name="busco_mode"> 226 <conditional name="busco_mode">
230 <param name="mode" value="prot" /> 227 <param name="mode" value="prot"/>
231 </conditional> 228 </conditional>
232 <param name="outputs" value="short_summary,missing,image,gff" /> 229 <param name="outputs" value="short_summary,missing,image,gff"/>
233 <output name="busco_sum"> 230 <output name="busco_sum">
234 <assert_contents> 231 <assert_contents>
235 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 232 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
236 <has_text text="BUSCO was run in mode: proteins" /> 233 <has_text text="BUSCO was run in mode: proteins"/>
237 </assert_contents> 234 </assert_contents>
238 </output> 235 </output>
239 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" /> 236 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/>
240 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" /> 237 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
241 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> 238 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/>
242 <output name="busco_gff"> 239 <output name="busco_gff">
243 <assert_contents> 240 <assert_contents>
244 <has_n_lines n="1"/> 241 <has_n_lines n="1"/>
245 <has_text text="##gff-version 3" /> 242 <has_text text="##gff-version 3"/>
246 </assert_contents> 243 </assert_contents>
247 </output> 244 </output>
248 </test> 245 </test>
249 <test expect_num_outputs="5"> 246 <test expect_num_outputs="5">
250 <param name="input" value="transcriptome.fa" /> 247 <param name="input" value="transcriptome.fa"/>
251 <conditional name="lineage"> 248 <conditional name="lineage">
252 <param name="lineage_mode" value="select_lineage" /> 249 <param name="lineage_mode" value="select_lineage"/>
253 <param name="lineage_dataset" value="arthropoda_odb10" /> 250 <param name="lineage_dataset" value="arthropoda_odb10"/>
254 </conditional> 251 </conditional>
255 <conditional name="busco_mode"> 252 <conditional name="busco_mode">
256 <param name="mode" value="tran" /> 253 <param name="mode" value="tran"/>
257 </conditional> 254 </conditional>
258 <param name="outputs" value="short_summary,missing,image,gff" /> 255 <param name="outputs" value="short_summary,missing,image,gff"/>
259 <output name="busco_sum"> 256 <output name="busco_sum">
260 <assert_contents> 257 <assert_contents>
261 <has_text text="BUSCO was run in mode: euk_tran" /> 258 <has_text text="BUSCO was run in mode: euk_tran"/>
262 </assert_contents> 259 </assert_contents>
263 </output> 260 </output>
264 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> 261 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/>
265 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> 262 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/>
266 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 263 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/>
267 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> 264 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/>
268 </test> 265 </test>
269 <test expect_num_outputs="3"> 266 <test expect_num_outputs="3">
270 <param name="input" value="genome.fa" /> 267 <param name="input" value="genome.fa"/>
271 <conditional name="lineage"> 268 <conditional name="lineage">
272 <param name="lineage_mode" value="select_lineage" /> 269 <param name="lineage_mode" value="select_lineage"/>
273 <param name="lineage_dataset" value="arthropoda_odb10" /> 270 <param name="lineage_dataset" value="arthropoda_odb10"/>
274 </conditional> 271 </conditional>
275 <conditional name="busco_mode"> 272 <conditional name="busco_mode">
276 <param name="mode" value="geno" /> 273 <param name="mode" value="geno"/>
277 <conditional name="use_augustus"> 274 <conditional name="use_augustus">
278 <param name="use_augustus_selector" value="augustus" /> 275 <param name="use_augustus_selector" value="augustus"/>
279 <conditional name="aug_prediction"> 276 <conditional name="aug_prediction">
280 <param name="augustus_mode" value="builtin" /> 277 <param name="augustus_mode" value="builtin"/>
281 <param name="augustus_species" value="human" /> 278 <param name="augustus_species" value="human"/>
282 </conditional> 279 </conditional>
283 </conditional> 280 </conditional>
284 </conditional> 281 </conditional>
285 <param name="outputs" value="short_summary,gff" /> 282 <param name="outputs" value="short_summary,gff"/>
286 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> 283 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
287 <assert_contents> 284 <assert_contents>
288 <has_text text="# Gene predictor used: augustus"/> 285 <has_text text="# Gene predictor used: augustus"/>
289 </assert_contents> 286 </assert_contents>
290 </output> 287 </output>
291 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> 288 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
292 <output name="busco_gff"> 289 <output name="busco_gff">
293 <assert_contents> 290 <assert_contents>
294 <has_n_lines n="1"/> 291 <has_n_lines n="1"/>
295 <has_text text="##gff-version 3" /> 292 <has_text text="##gff-version 3"/>
296 </assert_contents> 293 </assert_contents>
297 </output> 294 </output>
298 </test> 295 </test>
299 <test expect_num_outputs="3"> 296 <test expect_num_outputs="3">
300 <param name="input" value="genome.fa" /> 297 <param name="input" value="genome.fa"/>
301 <conditional name="lineage"> 298 <conditional name="lineage">
302 <param name="lineage_mode" value="select_lineage" /> 299 <param name="lineage_mode" value="select_lineage"/>
303 <param name="lineage_dataset" value="arthropoda_odb10" /> 300 <param name="lineage_dataset" value="arthropoda_odb10"/>
304 </conditional> 301 </conditional>
305 <conditional name="busco_mode"> 302 <conditional name="busco_mode">
306 <param name="mode" value="geno" /> 303 <param name="mode" value="geno"/>
307 <conditional name="use_augustus"> 304 <conditional name="use_augustus">
308 <param name="use_augustus_selector" value="augustus" /> 305 <param name="use_augustus_selector" value="augustus"/>
309 <conditional name="aug_prediction"> 306 <conditional name="aug_prediction">
310 <param name="augustus_mode" value="history" /> 307 <param name="augustus_mode" value="history"/>
311 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> 308 <param name="augustus_model" value="local.tar.gz" ftype="augustus"/>
312 </conditional> 309 </conditional>
313 </conditional> 310 </conditional>
314 </conditional> 311 </conditional>
315 <param name="outputs" value="short_summary,missing" /> 312 <param name="outputs" value="short_summary,missing"/>
316 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> 313 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
317 <assert_contents> 314 <assert_contents>
318 <has_text text="# Gene predictor used: augustus"/> 315 <has_text text="# Gene predictor used: augustus"/>
319 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 316 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
320 </assert_contents> 317 </assert_contents>
321 </output> 318 </output>
322 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> 319 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
323 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" /> 320 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
324 </test> 321 </test>
325 <test expect_num_outputs="5"> 322 <test expect_num_outputs="5">
326 <param name="input" value="genome.fa" /> 323 <param name="input" value="genome.fa"/>
327 <conditional name="lineage"> 324 <conditional name="lineage">
328 <param name="lineage_mode" value="select_lineage" /> 325 <param name="lineage_mode" value="select_lineage"/>
329 <param name="lineage_dataset" value="arthropoda_odb10" /> 326 <param name="lineage_dataset" value="arthropoda_odb10"/>
330 </conditional> 327 </conditional>
331 <conditional name="busco_mode"> 328 <conditional name="busco_mode">
332 <param name="mode" value="geno" /> 329 <param name="mode" value="geno"/>
333 <conditional name="use_augustus"> 330 <conditional name="use_augustus">
334 <param name="use_augustus_selector" value="metaeuk" /> 331 <param name="use_augustus_selector" value="metaeuk"/>
335 </conditional> 332 </conditional>
336 </conditional> 333 </conditional>
337 <param name="outputs" value="short_summary,missing,image,gff" /> 334 <param name="outputs" value="short_summary,missing,image,gff"/>
338 <output name="busco_sum"> 335 <output name="busco_sum">
339 <assert_contents> 336 <assert_contents>
340 <has_text text="# Gene predictor used: metaeuk"/> 337 <has_text text="# Gene predictor used: metaeuk"/>
341 </assert_contents> 338 </assert_contents>
342 </output> 339 </output>
351 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 348 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
352 <has_text text="9647at6656"/> 349 <has_text text="9647at6656"/>
353 </assert_contents> 350 </assert_contents>
354 </output> 351 </output>
355 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/> 352 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
356 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" /> 353 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
357 </test> 354 </test>
358 <test expect_num_outputs="5"> 355 <test expect_num_outputs="5">
359 <param name="input" value="genome.fa" /> 356 <param name="input" value="genome.fa"/>
360 <conditional name="lineage"> 357 <conditional name="lineage">
361 <param name="lineage_mode" value="auto_detect" /> 358 <param name="lineage_mode" value="auto_detect"/>
362 <param name="auto_lineage" value="--auto-lineage" /> 359 <param name="auto_lineage" value="--auto-lineage"/>
363 </conditional> 360 </conditional>
364 <conditional name="busco_mode"> 361 <conditional name="busco_mode">
365 <param name="mode" value="geno" /> 362 <param name="mode" value="geno"/>
366 <conditional name="use_augustus"> 363 <conditional name="use_augustus">
367 <param name="use_augustus_selector" value="metaeuk" /> 364 <param name="use_augustus_selector" value="metaeuk"/>
368 </conditional> 365 </conditional>
369 </conditional> 366 </conditional>
370 <param name="outputs" value="short_summary,missing,image,gff" /> 367 <param name="outputs" value="short_summary,missing,image,gff"/>
371 <output name="busco_sum"> 368 <output name="busco_sum">
372 <assert_contents> 369 <assert_contents>
373 <has_text text="Gene predictor used: metaeuk"/> 370 <has_text text="Gene predictor used: metaeuk"/>
374 </assert_contents> 371 </assert_contents>
375 </output> 372 </output>
383 <assert_contents> 380 <assert_contents>
384 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 381 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
385 <has_text text="The lineage dataset is: eukaryota_odb10"/> 382 <has_text text="The lineage dataset is: eukaryota_odb10"/>
386 </assert_contents> 383 </assert_contents>
387 </output> 384 </output>
388 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> 385 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
389 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> 386 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/>
390 </test> 387 </test>
391 <test expect_num_outputs="3"> 388 <test expect_num_outputs="3">
392 <param name="input" value="genome.fa" /> 389 <param name="input" value="genome.fa"/>
393 <conditional name="lineage"> 390 <conditional name="lineage">
394 <param name="lineage_mode" value="select_lineage" /> 391 <param name="lineage_mode" value="select_lineage"/>
395 <param name="lineage_dataset" value="arthropoda_odb10" /> 392 <param name="lineage_dataset" value="arthropoda_odb10"/>
396 </conditional> 393 </conditional>
397 <param name="outputs" value="short_summary,gff" /> 394 <param name="outputs" value="short_summary,gff"/>
398 <output name="busco_sum"> 395 <output name="busco_sum">
399 <assert_contents> 396 <assert_contents>
400 <has_text text="# Gene predictor used: miniprot"/> 397 <has_text text="# Gene predictor used: miniprot"/>
401 </assert_contents> 398 </assert_contents>
402 </output> 399 </output>
403 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" /> 400 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>
404 <output name="busco_table" file="genome_results_miniprot/full_table"> 401 <output name="busco_table" file="genome_results_miniprot/full_table">
405 <assert_contents> 402 <assert_contents>
406 <has_text text="# BUSCO version is: @TOOL_VERSION@"/> 403 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
407 <has_text text="9647at6656"/> 404 <has_text text="9647at6656"/>
408 </assert_contents> 405 </assert_contents>
410 </test> 407 </test>
411 </tests> 408 </tests>
412 <help><![CDATA[ 409 <help><![CDATA[
413 410
414 411
415 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs 412 BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
416 -------------------------------------------------------------------------------------------------------------- 413 --------------------------------------------------------------------------------------------------------------
417 414
418 Interpreting the results 415 Interpreting the results
419 ^^^^^^^^^^^^^^^^^^^^^^^^ 416 ^^^^^^^^^^^^^^^^^^^^^^^^
420 417
430 Therefore you should filter them before a BUSCO analysis. 427 Therefore you should filter them before a BUSCO analysis.
431 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment 428 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
432 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples 429 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
433 is what you will be aiming for. 430 is what you will be aiming for.
434 431
435 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_ 432 For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
436 . 433 .
437 434
438 .. _BUSCO: http://busco.ezlab.org/ 435 .. _BUSCO: http://busco.ezlab.org/
439 436
440 ]]> </help> 437 ]]></help>
441 <expand macro="citations" /> 438 <expand macro="citations"/>
442 </tool> 439 </tool>