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comparison flye.xml @ 12:6e5b72b4e1fb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit fb1299282c85caf05328489921813aefdf83ff26
author bgruening
date Wed, 04 Dec 2024 22:12:31 +0000
parents 7066276883d6
children 5ac579ded893
comparison
equal deleted inserted replaced
11:dba2d77852ee 12:6e5b72b4e1fb
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 ${on_string}: assembly graph"/>
108 <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/> 108 <data name="assembly_gfa" format="gfa1" from_work_dir="out_dir/assembly_graph.gfa" label="${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>
114 <tests> 114 <tests>
115 <!--Test 01: pacbio-raw--> 115 <!--Test 01: pacbio-raw-->
116 <test expect_num_outputs="5"> 116 <test expect_num_outputs="5">
117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/> 117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
118 <param name="mode" value="--pacbio-raw"/> 118 <conditional name="mode_conditional">
119 <param name="mode" value="--pacbio-raw"/>
120 </conditional>
119 <param name="iterations" value="0"/> 121 <param name="iterations" value="0"/>
120 <param name="generate_log" value="true"/> 122 <param name="generate_log" value="true"/>
121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> 123 <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"/> 124 <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="gfa" compare="diff" lines_diff="10"/> 125 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa1" compare="diff" lines_diff="10"/>
124 <output name="consensus" ftype="fasta"> 126 <output name="consensus" ftype="fasta">
125 <assert_contents> 127 <assert_contents>
126 <has_line line=">contig_1"/> 128 <has_line line=">contig_1"/>
127 </assert_contents> 129 </assert_contents>
128 </output> 130 </output>
129 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/> 131 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
130 </test> 132 </test>
131 <!--Test 02: nano raw--> 133 <!--Test 02: nano raw-->
132 <test expect_num_outputs="4"> 134 <test expect_num_outputs="4">
133 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> 135 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
134 <param name="mode" value="--nano-raw"/> 136 <conditional name="mode_conditional">
137 <param name="mode" value="--nano-raw"/>
138 </conditional>
135 <param name="iterations" value="0"/> 139 <param name="iterations" value="0"/>
136 <output name="assembly_info" ftype="tabular"> 140 <output name="assembly_info" ftype="tabular">
137 <assert_contents> 141 <assert_contents>
138 <has_size value="95" delta="100"/> 142 <has_size value="95" delta="100"/>
139 </assert_contents> 143 </assert_contents>
141 <output name="assembly_graph" ftype="graph_dot"> 145 <output name="assembly_graph" ftype="graph_dot">
142 <assert_contents> 146 <assert_contents>
143 <has_size value="803" delta="100"/> 147 <has_size value="803" delta="100"/>
144 </assert_contents> 148 </assert_contents>
145 </output> 149 </output>
146 <output name="assembly_gfa" ftype="gfa"> 150 <output name="assembly_gfa" ftype="gfa1">
147 <assert_contents> 151 <assert_contents>
148 <has_size value="35047" delta="100"/> 152 <has_size value="35047" delta="100"/>
149 </assert_contents> 153 </assert_contents>
150 </output> 154 </output>
151 <output name="consensus" ftype="fasta"> 155 <output name="consensus" ftype="fasta">
160 <conditional name="mode_conditional"> 164 <conditional name="mode_conditional">
161 <param name="mode" value="--nano-raw"/> 165 <param name="mode" value="--nano-raw"/>
162 </conditional> 166 </conditional>
163 <conditional name="asm"> 167 <conditional name="asm">
164 <param name="asm_select" value="true" /> 168 <param name="asm_select" value="true" />
165 <param name="asm" value="30"/> 169 <param name="asm_coverage" value="30"/>
166 <param name="genome_size" value="3980000"/> 170 <param name="genome_size" value="3980000"/>
167 </conditional> 171 </conditional>
168 <output name="assembly_info" ftype="tabular"> 172 <output name="assembly_info" ftype="tabular">
169 <assert_contents> 173 <assert_contents>
170 <has_size value="286" delta="100"/> 174 <has_size value="286" delta="100"/>
173 <output name="assembly_graph" ftype="graph_dot"> 177 <output name="assembly_graph" ftype="graph_dot">
174 <assert_contents> 178 <assert_contents>
175 <has_size value="1840" delta="100"/> 179 <has_size value="1840" delta="100"/>
176 </assert_contents> 180 </assert_contents>
177 </output> 181 </output>
178 <output name="assembly_gfa" ftype="gfa"> 182 <output name="assembly_gfa" ftype="gfa1">
179 <assert_contents> 183 <assert_contents>
180 <has_size value="420752" delta="100"/> 184 <has_size value="420752" delta="100"/>
181 </assert_contents> 185 </assert_contents>
182 </output> 186 </output>
183 <output name="consensus" ftype="fasta"> 187 <output name="consensus" ftype="fasta">
201 <output name="assembly_graph" ftype="graph_dot"> 205 <output name="assembly_graph" ftype="graph_dot">
202 <assert_contents> 206 <assert_contents>
203 <has_size value="367" delta="100"/> 207 <has_size value="367" delta="100"/>
204 </assert_contents> 208 </assert_contents>
205 </output> 209 </output>
206 <output name="assembly_gfa" ftype="gfa"> 210 <output name="assembly_gfa" ftype="gfa1">
207 <assert_contents> 211 <assert_contents>
208 <has_size value="418729" delta="100"/> 212 <has_size value="418729" delta="100"/>
209 </assert_contents> 213 </assert_contents>
210 </output> 214 </output>
211 <output name="consensus" ftype="fasta"> 215 <output name="consensus" ftype="fasta">
229 <output name="assembly_graph" ftype="graph_dot"> 233 <output name="assembly_graph" ftype="graph_dot">
230 <assert_contents> 234 <assert_contents>
231 <has_size value="1248" delta="100"/> 235 <has_size value="1248" delta="100"/>
232 </assert_contents> 236 </assert_contents>
233 </output> 237 </output>
234 <output name="assembly_gfa" ftype="gfa"> 238 <output name="assembly_gfa" ftype="gfa1">
235 <assert_contents> 239 <assert_contents>
236 <has_size value="419414" delta="1000"/> 240 <has_size value="419414" delta="1000"/>
237 </assert_contents> 241 </assert_contents>
238 </output> 242 </output>
239 <output name="consensus" ftype="fasta"> 243 <output name="consensus" ftype="fasta">
258 <output name="assembly_graph" ftype="graph_dot"> 262 <output name="assembly_graph" ftype="graph_dot">
259 <assert_contents> 263 <assert_contents>
260 <has_size value="1248" delta="500"/> 264 <has_size value="1248" delta="500"/>
261 </assert_contents> 265 </assert_contents>
262 </output> 266 </output>
263 <output name="assembly_gfa" ftype="gfa"> 267 <output name="assembly_gfa" ftype="gfa1">
264 <assert_contents> 268 <assert_contents>
265 <has_size value="420254" delta="2000"/> 269 <has_size value="420254" delta="2000"/>
266 </assert_contents> 270 </assert_contents>
267 </output> 271 </output>
268 <output name="consensus" ftype="fasta"> 272 <output name="consensus" ftype="fasta">
274 <!--Test 07: keep haplotypes--> 278 <!--Test 07: keep haplotypes-->
275 <test expect_num_outputs="4"> 279 <test expect_num_outputs="4">
276 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> 280 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
277 <conditional name="mode_conditional"> 281 <conditional name="mode_conditional">
278 <param name="mode" value="--pacbio-corr"/> 282 <param name="mode" value="--pacbio-corr"/>
279 <param name="hifi_error" value="0.21"/>
280 </conditional> 283 </conditional>
281 <param name="min_overlap" value="1000"/> 284 <param name="min_overlap" value="1000"/>
282 <param name="keep-haplotypes" value="true"/> 285 <param name="keep_haplotypes" value="true"/>
283 <output name="assembly_info" ftype="tabular"> 286 <output name="assembly_info" ftype="tabular">
284 <assert_contents> 287 <assert_contents>
285 <has_size value="286" delta="200"/> 288 <has_size value="286" delta="200"/>
286 </assert_contents> 289 </assert_contents>
287 </output> 290 </output>
288 <output name="assembly_graph" ftype="graph_dot"> 291 <output name="assembly_graph" ftype="graph_dot">
289 <assert_contents> 292 <assert_contents>
290 <has_size value="1273" delta="500"/> 293 <has_size value="1273" delta="500"/>
291 </assert_contents> 294 </assert_contents>
292 </output> 295 </output>
293 <output name="assembly_gfa" ftype="gfa"> 296 <output name="assembly_gfa" ftype="gfa1">
294 <assert_contents> 297 <assert_contents>
295 <has_size value="420254" delta="3000"/> 298 <has_size value="420254" delta="3000"/>
296 </assert_contents> 299 </assert_contents>
297 </output> 300 </output>
298 <output name="consensus" ftype="fasta"> 301 <output name="consensus" ftype="fasta">
302 </output> 305 </output>
303 </test> 306 </test>
304 <!--Test 08: scaffolding mode--> 307 <!--Test 08: scaffolding mode-->
305 <test expect_num_outputs="4"> 308 <test expect_num_outputs="4">
306 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> 309 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
307 <param name="mode" value="--nano-hq"/> 310 <conditional name="mode_conditional">
311 <param name="mode" value="--nano-hq"/>
312 </conditional>
308 <param name="min_overlap" value="1000"/> 313 <param name="min_overlap" value="1000"/>
309 <param name="scaffold" value="true"/> 314 <param name="scaffold" value="true"/>
310 <output name="assembly_info" ftype="tabular"> 315 <output name="assembly_info" ftype="tabular">
311 <assert_contents> 316 <assert_contents>
312 <has_size value="286" delta="100"/> 317 <has_size value="286" delta="100"/>
315 <output name="assembly_graph" ftype="graph_dot"> 320 <output name="assembly_graph" ftype="graph_dot">
316 <assert_contents> 321 <assert_contents>
317 <has_size value="1248" delta="100"/> 322 <has_size value="1248" delta="100"/>
318 </assert_contents> 323 </assert_contents>
319 </output> 324 </output>
320 <output name="assembly_gfa" ftype="gfa"> 325 <output name="assembly_gfa" ftype="gfa1">
321 <assert_contents> 326 <assert_contents>
322 <has_size value="419414" delta="2000"/> 327 <has_size value="419414" delta="2000"/>
323 </assert_contents> 328 </assert_contents>
324 </output> 329 </output>
325 <output name="consensus" ftype="fasta"> 330 <output name="consensus" ftype="fasta">
329 </output> 334 </output>
330 </test> 335 </test>
331 <!--Test 09: test not-alt-contigs parameter w--> 336 <!--Test 09: test not-alt-contigs parameter w-->
332 <test expect_num_outputs="4"> 337 <test expect_num_outputs="4">
333 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> 338 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
334 <param name="mode" value="--nano-raw"/> 339 <conditional name="mode_conditional">
340 <param name="mode" value="--nano-raw"/>
341 </conditional>
335 <param name="iterations" value="0"/> 342 <param name="iterations" value="0"/>
336 <param name="no_alt_contigs" value="true"/> 343 <param name="no_alt_contigs" value="true"/>
337 <output name="assembly_info" ftype="tabular"> 344 <output name="assembly_info" ftype="tabular">
338 <assert_contents> 345 <assert_contents>
339 <has_size value="151" delta="100"/> 346 <has_size value="151" delta="100"/>
342 <output name="assembly_graph" ftype="graph_dot"> 349 <output name="assembly_graph" ftype="graph_dot">
343 <assert_contents> 350 <assert_contents>
344 <has_size value="217" delta="100"/> 351 <has_size value="217" delta="100"/>
345 </assert_contents> 352 </assert_contents>
346 </output> 353 </output>
347 <output name="assembly_gfa" ftype="gfa"> 354 <output name="assembly_gfa" ftype="gfa1">
348 <assert_contents> 355 <assert_contents>
349 <has_size value="5110" delta="100"/> 356 <has_size value="5110" delta="100"/>
350 </assert_contents> 357 </assert_contents>
351 </output> 358 </output>
352 <output name="consensus" ftype="fasta"> 359 <output name="consensus" ftype="fasta">