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comparison flye.xml @ 12:3e4f8642c77e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author bgruening
date Mon, 26 Aug 2024 13:54:31 +0000
parents 291923e6f276
children
comparison
equal deleted inserted replaced
11:291923e6f276 12:3e4f8642c77e
103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/> 103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
104 </inputs> 104 </inputs>
105 <outputs> 105 <outputs>
106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/> 106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/> 107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
108 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/> 108 <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/> 109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log"> 110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
111 <filter>generate_log</filter> 111 <filter>generate_log</filter>
112 </data> 112 </data>
113 </outputs> 113 </outputs>
118 <param name="mode" value="--pacbio-raw"/> 118 <param name="mode" value="--pacbio-raw"/>
119 <param name="iterations" value="0"/> 119 <param name="iterations" value="0"/>
120 <param name="generate_log" value="true"/> 120 <param name="generate_log" value="true"/>
121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> 121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>
124 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/> 124 <output name="consensus" ftype="fasta">
125 <assert_contents>
126 <has_line line=">contig_1"/>
127 </assert_contents>
128 </output>
125 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/> 129 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
126 </test> 130 </test>
127 <!--Test 02: nano raw--> 131 <!--Test 02: nano raw-->
128 <test expect_num_outputs="4"> 132 <test expect_num_outputs="4">
129 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> 133 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
137 <output name="assembly_graph" ftype="graph_dot"> 141 <output name="assembly_graph" ftype="graph_dot">
138 <assert_contents> 142 <assert_contents>
139 <has_size value="803" delta="100"/> 143 <has_size value="803" delta="100"/>
140 </assert_contents> 144 </assert_contents>
141 </output> 145 </output>
142 <output name="assembly_gfa" ftype="txt"> 146 <output name="assembly_gfa" ftype="gfa">
143 <assert_contents> 147 <assert_contents>
144 <has_size value="35047" delta="100"/> 148 <has_size value="35047" delta="100"/>
145 </assert_contents> 149 </assert_contents>
146 </output> 150 </output>
147 <output name="consensus" ftype="fasta"> 151 <output name="consensus" ftype="fasta">
169 <output name="assembly_graph" ftype="graph_dot"> 173 <output name="assembly_graph" ftype="graph_dot">
170 <assert_contents> 174 <assert_contents>
171 <has_size value="1840" delta="100"/> 175 <has_size value="1840" delta="100"/>
172 </assert_contents> 176 </assert_contents>
173 </output> 177 </output>
174 <output name="assembly_gfa" ftype="txt"> 178 <output name="assembly_gfa" ftype="gfa">
175 <assert_contents> 179 <assert_contents>
176 <has_size value="420752" delta="100"/> 180 <has_size value="420752" delta="100"/>
177 </assert_contents> 181 </assert_contents>
178 </output> 182 </output>
179 <output name="consensus" ftype="fasta"> 183 <output name="consensus" ftype="fasta">
197 <output name="assembly_graph" ftype="graph_dot"> 201 <output name="assembly_graph" ftype="graph_dot">
198 <assert_contents> 202 <assert_contents>
199 <has_size value="367" delta="100"/> 203 <has_size value="367" delta="100"/>
200 </assert_contents> 204 </assert_contents>
201 </output> 205 </output>
202 <output name="assembly_gfa" ftype="txt"> 206 <output name="assembly_gfa" ftype="gfa">
203 <assert_contents> 207 <assert_contents>
204 <has_size value="418729" delta="100"/> 208 <has_size value="418729" delta="100"/>
205 </assert_contents> 209 </assert_contents>
206 </output> 210 </output>
207 <output name="consensus" ftype="fasta"> 211 <output name="consensus" ftype="fasta">
225 <output name="assembly_graph" ftype="graph_dot"> 229 <output name="assembly_graph" ftype="graph_dot">
226 <assert_contents> 230 <assert_contents>
227 <has_size value="1248" delta="100"/> 231 <has_size value="1248" delta="100"/>
228 </assert_contents> 232 </assert_contents>
229 </output> 233 </output>
230 <output name="assembly_gfa" ftype="txt"> 234 <output name="assembly_gfa" ftype="gfa">
231 <assert_contents> 235 <assert_contents>
232 <has_size value="419414" delta="100"/> 236 <has_size value="419414" delta="1000"/>
233 </assert_contents> 237 </assert_contents>
234 </output> 238 </output>
235 <output name="consensus" ftype="fasta"> 239 <output name="consensus" ftype="fasta">
236 <assert_contents> 240 <assert_contents>
237 <has_size value="426277" delta="100"/> 241 <has_size value="426277" delta="1000"/>
238 </assert_contents> 242 </assert_contents>
239 </output> 243 </output>
240 </test> 244 </test>
241 <!--Test 06: hifi error option--> 245 <!--Test 06: hifi error option-->
242 <test expect_num_outputs="4"> 246 <test expect_num_outputs="4">
251 <has_size value="286" delta="100"/> 255 <has_size value="286" delta="100"/>
252 </assert_contents> 256 </assert_contents>
253 </output> 257 </output>
254 <output name="assembly_graph" ftype="graph_dot"> 258 <output name="assembly_graph" ftype="graph_dot">
255 <assert_contents> 259 <assert_contents>
256 <has_size value="1500" delta="100"/> 260 <has_size value="1248" delta="500"/>
257 </assert_contents> 261 </assert_contents>
258 </output> 262 </output>
259 <output name="assembly_gfa" ftype="txt"> 263 <output name="assembly_gfa" ftype="gfa">
260 <assert_contents> 264 <assert_contents>
261 <has_size value="418422" delta="100"/> 265 <has_size value="420254" delta="2000"/>
262 </assert_contents> 266 </assert_contents>
263 </output> 267 </output>
264 <output name="consensus" ftype="fasta"> 268 <output name="consensus" ftype="fasta">
265 <assert_contents> 269 <assert_contents>
266 <has_size value="425147" delta="200"/> 270 <has_size value="427131" delta="2000"/>
267 </assert_contents> 271 </assert_contents>
268 </output> 272 </output>
269 </test> 273 </test>
270 <!--Test 07: keep haplotypes--> 274 <!--Test 07: keep haplotypes-->
271 <test expect_num_outputs="4"> 275 <test expect_num_outputs="4">
276 </conditional> 280 </conditional>
277 <param name="min_overlap" value="1000"/> 281 <param name="min_overlap" value="1000"/>
278 <param name="keep-haplotypes" value="true"/> 282 <param name="keep-haplotypes" value="true"/>
279 <output name="assembly_info" ftype="tabular"> 283 <output name="assembly_info" ftype="tabular">
280 <assert_contents> 284 <assert_contents>
281 <has_size value="286" delta="100"/> 285 <has_size value="286" delta="200"/>
282 </assert_contents> 286 </assert_contents>
283 </output> 287 </output>
284 <output name="assembly_graph" ftype="graph_dot"> 288 <output name="assembly_graph" ftype="graph_dot">
285 <assert_contents> 289 <assert_contents>
286 <has_size value="1273" delta="100"/> 290 <has_size value="1273" delta="500"/>
287 </assert_contents> 291 </assert_contents>
288 </output> 292 </output>
289 <output name="assembly_gfa" ftype="txt"> 293 <output name="assembly_gfa" ftype="gfa">
290 <assert_contents> 294 <assert_contents>
291 <has_size value="418511" delta="100"/> 295 <has_size value="420254" delta="3000"/>
292 </assert_contents> 296 </assert_contents>
293 </output> 297 </output>
294 <output name="consensus" ftype="fasta"> 298 <output name="consensus" ftype="fasta">
295 <assert_contents> 299 <assert_contents>
296 <has_size value="425267" delta="100"/> 300 <has_size value="427131" delta="3000"/>
297 </assert_contents> 301 </assert_contents>
298 </output> 302 </output>
299 </test> 303 </test>
300 <!--Test 08: scaffolding mode--> 304 <!--Test 08: scaffolding mode-->
301 <test expect_num_outputs="4"> 305 <test expect_num_outputs="4">
311 <output name="assembly_graph" ftype="graph_dot"> 315 <output name="assembly_graph" ftype="graph_dot">
312 <assert_contents> 316 <assert_contents>
313 <has_size value="1248" delta="100"/> 317 <has_size value="1248" delta="100"/>
314 </assert_contents> 318 </assert_contents>
315 </output> 319 </output>
316 <output name="assembly_gfa" ftype="txt"> 320 <output name="assembly_gfa" ftype="gfa">
317 <assert_contents> 321 <assert_contents>
318 <has_size value="419414" delta="1000"/> 322 <has_size value="419414" delta="2000"/>
319 </assert_contents> 323 </assert_contents>
320 </output> 324 </output>
321 <output name="consensus" ftype="fasta"> 325 <output name="consensus" ftype="fasta">
322 <assert_contents> 326 <assert_contents>
323 <has_size value="426277" delta="1000"/> 327 <has_size value="426277" delta="2000"/>
324 </assert_contents> 328 </assert_contents>
325 </output> 329 </output>
326 </test> 330 </test>
327 <!--Test 09: test not-alt-contigs parameter w--> 331 <!--Test 09: test not-alt-contigs parameter w-->
328 <test expect_num_outputs="4"> 332 <test expect_num_outputs="4">
338 <output name="assembly_graph" ftype="graph_dot"> 342 <output name="assembly_graph" ftype="graph_dot">
339 <assert_contents> 343 <assert_contents>
340 <has_size value="217" delta="100"/> 344 <has_size value="217" delta="100"/>
341 </assert_contents> 345 </assert_contents>
342 </output> 346 </output>
343 <output name="assembly_gfa" ftype="txt"> 347 <output name="assembly_gfa" ftype="gfa">
344 <assert_contents> 348 <assert_contents>
345 <has_size value="5110" delta="100"/> 349 <has_size value="5110" delta="100"/>
346 </assert_contents> 350 </assert_contents>
347 </output> 351 </output>
348 <output name="consensus" ftype="fasta"> 352 <output name="consensus" ftype="fasta">