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comparison merqury.xml @ 1:39edec572bae draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
author iuc
date Thu, 11 Nov 2021 16:38:42 +0000
parents 9d79beb19ac3
children 589078edd230
comparison
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0:9d79beb19ac3 1:39edec572bae
1 <tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01"> 1 <tool id="merqury" name="Merqury" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>evaluate the assembly quality</description> 2 <description>evaluate the assembly quality</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <version_command>merqury --version</version_command> 8 <version_command>merqury --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 mkdir -p output_files 10 mkdir -p output_files
11 #if $mode.options == 'default' 11 #if $mode.options == 'default'
135 <valid initial="string.letters,string.digits"> 135 <valid initial="string.letters,string.digits">
136 <add value="_" /> 136 <add value="_" />
137 </valid> 137 </valid>
138 </sanitizer> 138 </sanitizer>
139 </param> 139 </param>
140 <param name="output_selector" type="select" display="checkboxes" multiple="true" optional="true" label="Output options">
141 <option value="qv" selected="true">QV stats</option>
142 <option value="plots" selected="true">Plots</option>
143 <option value="sizes">Size files</option>
144 <option value="stats" selected="true">Stats file</option>
145 <option value="bed">BED: hap-mer tracks</option>
146 <option value="wig">WIG: hap-mer tracks</option>
147 </param>
140 </inputs> 148 </inputs>
141 <outputs> 149 <outputs>
142 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed"> 150 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
143 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/> 151 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
144 </collection> 152 <filter>"bed" in output_selector</filter>
145 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig"> 153 </collection>
154 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
146 <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/> 155 <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
147 </collection> 156 <filter>"wig" in output_selector</filter>
148 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv"> 157 </collection>
158 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
149 <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/> 159 <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
150 </collection> 160 <filter>"qv" in output_selector</filter>
151 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png"> 161 </collection>
162 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
152 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/> 163 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
164 <filter>"plots" in output_selector</filter>
153 </collection> 165 </collection>
154 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files"> 166 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
155 <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/> 167 <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
168 <filter>"sizes" in output_selector</filter>
156 </collection> 169 </collection>
157 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats"> 170 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
158 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/> 171 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
172 <filter>"stats" in output_selector</filter>
159 </collection> 173 </collection>
160 </outputs> 174 </outputs>
161 <tests> 175 <tests>
162 <test> 176 <!--Test 01: trio mode-->
177 <test expect_num_outputs="2">
163 <conditional name="mode"> 178 <conditional name="mode">
164 <param name="options" value="trio"/> 179 <param name="options" value="trio"/>
165 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/> 180 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
166 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/> 181 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
167 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/> 182 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
169 <param name="number_assemblies" value="one"/> 184 <param name="number_assemblies" value="one"/>
170 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> 185 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
171 </conditional> 186 </conditional>
172 </conditional> 187 </conditional>
173 <param name="label" value="output_01"/> 188 <param name="label" value="output_01"/>
174 <output_collection name="png_files" type="list" count="3"> 189 <param name="output_selector" value="sizes"/>
175 <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
176 <assert_contents>
177 <has_size value="2733" delta="100"/>
178 </assert_contents>
179 </element>
180 <element name="output_01.assembly.pat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
181 <assert_contents>
182 <has_size value="2733" delta="100"/>
183 </assert_contents>
184 </element>
185 <element name="output_01.hapmers.blob" file="output_01.hapmers.blob.png" ftype="png">
186 <assert_contents>
187 <has_size value="10764" delta="100"/>
188 </assert_contents>
189 </element>
190 </output_collection>
191 <output_collection name="stats_files" type="list" count="2">
192 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
193 <element name="output_01.completeness" ftype="tabular"/>
194 </output_collection>
195 <output_collection name="wig_files" type="list" count="2">
196 <element name="output_01.assembly.pat" ftype="wig"/>
197 <element name="output_01.assembly.mat" file="output_01.assembly.mat.wig" ftype="wig"/>
198 </output_collection>
199 <output_collection name="sizes_files" type="list" count="2"> 190 <output_collection name="sizes_files" type="list" count="2">
200 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/> 191 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
201 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/> 192 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
202 </output_collection> 193 </output_collection>
203 <output_collection name="bed_files" type="list" count="3">
204 <element name="output_01.assembly.100_20000.phased_block" ftype="bed"/>
205 <element name="output_01.assembly.100_20000.switch" ftype="bed"/>
206 <element name="output_01.assembly.sort"/>
207 </output_collection>
208 </test> 194 </test>
209 <test> 195 <!--Test 02: standard mode-->
196 <test expect_num_outputs="11">
210 <conditional name="mode"> 197 <conditional name="mode">
211 <param name="options" value="default"/> 198 <param name="options" value="default"/>
212 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/> 199 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
213 <conditional name="assembly_options"> 200 <conditional name="assembly_options">
214 <param name="number_assemblies" value="one"/> 201 <param name="number_assemblies" value="one"/>
215 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> 202 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
216 </conditional> 203 </conditional>
217 </conditional> 204 </conditional>
218 <param name="label" value="output_02"/> 205 <param name="label" value="output_02"/>
206 <param name="output_selector" value="qv,png,bed,wig,sizes,stats"/>
207 <param name="output_selector" value="plots,stats,wig,sizes,bed"/>
219 <output_collection name="png_files" type="list" count="6"> 208 <output_collection name="png_files" type="list" count="6">
220 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png"> 209 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
221 <assert_contents> 210 <assert_contents>
222 <has_size value="58059" delta="100"/> 211 <has_size value="71874" delta="100"/>
223 </assert_contents> 212 </assert_contents>
224 </element> 213 </element>
225 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png"> 214 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
226 <assert_contents> 215 <assert_contents>
227 <has_size value="57763" delta="100"/> 216 <has_size value="71888" delta="100"/>
228 </assert_contents> 217 </assert_contents>
229 </element> 218 </element>
230 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png"> 219 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
231 <assert_contents> 220 <assert_contents>
232 <has_size value="61814" delta="100"/> 221 <has_size value="71123" delta="100"/>
233 </assert_contents> 222 </assert_contents>
234 </element> 223 </element>
235 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png"> 224 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
236 <assert_contents> 225 <assert_contents>
237 <has_size value="64445" delta="100"/> 226 <has_size value="47245" delta="100"/>
238 </assert_contents> 227 </assert_contents>
239 </element> 228 </element>
240 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png"> 229 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
241 <assert_contents> 230 <assert_contents>
242 <has_size value="64795" delta="100"/> 231 <has_size value="46896" delta="100"/>
243 </assert_contents> 232 </assert_contents>
244 </element> 233 </element>
245 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png"> 234 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
246 <assert_contents> 235 <assert_contents>
247 <has_size value="66317" delta="100"/> 236 <has_size value="45945" delta="100"/>
248 </assert_contents> 237 </assert_contents>
249 </element> 238 </element>
250 </output_collection> 239 </output_collection>
251 <output_collection name="stats_files" type="list" count="1"> 240 <output_collection name="stats_files" type="list" count="1">
252 <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/> 241 <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>
256 <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/> 245 <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
257 </output_collection> 246 </output_collection>
258 <output_collection name="wig_files" type="list" count="1"> 247 <output_collection name="wig_files" type="list" count="1">
259 <element name="assembly_only" ftype="wig"> 248 <element name="assembly_only" ftype="wig">
260 <assert_contents> 249 <assert_contents>
261 <has_size value="29909811" delta="100"/> 250 <has_size value="0"/>
262 </assert_contents> 251 </assert_contents>
263 </element> 252 </element>
264 </output_collection> 253 </output_collection>
265 <output_collection name="bed_files" type="list" count="1"> 254 <output_collection name="bed_files" type="list" count="1">
266 <element name="assembly_only" ftype="bed"> 255 <element name="assembly_only" ftype="bed">
267 <assert_contents> 256 <assert_contents>
268 <has_size value="73516121" delta="100"/> 257 <has_size value="0"/>
269 </assert_contents> 258 </assert_contents>
270 </element> 259 </element>
271 </output_collection> 260 </output_collection>
272 </test> 261 </test>
273 <test> 262 <!--Test 03: Standard mode two assemblies-->
263 <test expect_num_outputs="4">
274 <conditional name="mode"> 264 <conditional name="mode">
275 <param name="options" value="default"/> 265 <param name="options" value="default"/>
276 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/> 266 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
277 <conditional name="assembly_options"> 267 <conditional name="assembly_options">
278 <param name="number_assemblies" value="two"/> 268 <param name="number_assemblies" value="two"/>
279 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> 269 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
280 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/> 270 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
281 </conditional> 271 </conditional>
282 </conditional> 272 </conditional>
283 <param name="label" value="output_03"/> 273 <param name="label" value="output_03"/>
284 <output_collection name="png_files" type="list" count="10"> 274 <param name="output_selector" value="qv,stats"/>
285 <element name="output_03.assembly_01.spectra-cn.fl" file="output_03.assembly_01.spectra-cn.fl.png" ftype="png">
286 <assert_contents>
287 <has_size value="58059" delta="100"/>
288 </assert_contents>
289 </element>
290 <element name="output_03.assembly_01.spectra-cn.ln" file="output_03.assembly_01.spectra-cn.ln.png" ftype="png">
291 <assert_contents>
292 <has_size value="57763" delta="100"/>
293 </assert_contents>
294 </element>
295 <element name="output_03.assembly_01.spectra-cn.st" file="output_03.assembly_01.spectra-cn.st.png" ftype="png">
296 <assert_contents>
297 <has_size value="61814" delta="100"/>
298 </assert_contents>
299 </element>
300 <element name="output_03.assembly_02.spectra-cn.fl" file="output_03.assembly_02.spectra-cn.fl.png" ftype="png">
301 <assert_contents>
302 <has_size value="61579" delta="100"/>
303 </assert_contents>
304 </element>
305 <element name="output_03.assembly_02.spectra-cn.ln" file="output_03.assembly_02.spectra-cn.ln.png" ftype="png">
306 <assert_contents>
307 <has_size value="61538" delta="100"/>
308 </assert_contents>
309 </element>
310 <element name="output_03.assembly_02.spectra-cn.st" file="output_03.assembly_02.spectra-cn.st.png" ftype="png">
311 <assert_contents>
312 <has_size value="67297" delta="100"/>
313 </assert_contents>
314 </element>
315 <element name="output_03.spectra-asm.ln" file="output_03.spectra-asm.ln.png" ftype="png">
316 <assert_contents>
317 <has_size value="2733" delta="100"/>
318 </assert_contents>
319 </element>
320 <element name="output_03.spectra-cn.fl" file="output_03.spectra-cn.fl.png" ftype="png">
321 <assert_contents>
322 <has_size value="61397" delta="100"/>
323 </assert_contents>
324 </element>
325 <element name="output_03.spectra-cn.ln" file="output_03.spectra-cn.ln.png" ftype="png">
326 <assert_contents>
327 <has_size value="61050" delta="100"/>
328 </assert_contents>
329 </element>
330 <element name="output_03.spectra-cn.st" file="output_03.spectra-cn.st.png" ftype="png">
331 <assert_contents>
332 <has_size value="65243" delta="100"/>
333 </assert_contents>
334 </element>
335 </output_collection>
336 <output_collection name="stats_files" type="list" count="1"> 275 <output_collection name="stats_files" type="list" count="1">
337 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/> 276 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
338 </output_collection> 277 </output_collection>
339 <output_collection name="qv_files" type="list" count="3"> 278 <output_collection name="qv_files" type="list" count="3">
340 <element name="output_03.assembly_01" ftype="tabular"/> 279 <element name="output_03.assembly_01" ftype="tabular"/>
341 <element name="output_03.assembly_02" ftype="tabular"/> 280 <element name="output_03.assembly_02" ftype="tabular"/>
342 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/> 281 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
343 </output_collection> 282 </output_collection>
344 </test> 283 </test>
345 <test> 284 <!--Test 04: trio mode two assemblies-->
285 <test expect_num_outputs="1">
346 <conditional name="mode"> 286 <conditional name="mode">
347 <param name="options" value="trio"/> 287 <param name="options" value="trio"/>
348 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/> 288 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
349 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/> 289 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
350 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/> 290 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
353 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> 293 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
354 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/> 294 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
355 </conditional> 295 </conditional>
356 </conditional> 296 </conditional>
357 <param name="label" value="output_04"/> 297 <param name="label" value="output_04"/>
358 <output_collection name="png_files" type="list" count="5"> 298 <param name="output_selector" value="qv"/>
359 <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">
360 <assert_contents>
361 <has_size value="2733" delta="100"/>
362 </assert_contents>
363 </element>
364 <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">
365 <assert_contents>
366 <has_size value="2733" delta="100"/>
367 </assert_contents>
368 </element>
369 <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">
370 <assert_contents>
371 <has_size value="2733" delta="100"/>
372 </assert_contents>
373 </element>
374 <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">
375 <assert_contents>
376 <has_size value="2733" delta="100"/>
377 </assert_contents>
378 </element>
379 <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">
380 <assert_contents>
381 <has_size value="10764" delta="100"/>
382 </assert_contents>
383 </element>
384 </output_collection>
385 <output_collection name="stats_files" type="list" count="3">
386 <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>
387 <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>
388 <element name="output_04.completeness"/>
389 </output_collection>
390 <output_collection name="qv_files" type="list" count="1"> 299 <output_collection name="qv_files" type="list" count="1">
391 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/> 300 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
392 </output_collection>
393 <output_collection name="wig_files" type="list" count="4">
394 <element name="output_04.assembly_01.pat" ftype="wig"/>
395 <element name="output_04.assembly_01.mat" ftype="wig"/>
396 <element name="output_04.assembly_02.pat" ftype="wig"/>
397 <element name="output_04.assembly_02.mat" ftype="wig"/>
398 </output_collection>
399 <output_collection name="sizes_files" type="list" count="4">
400 <element name="output_04.assembly_01.100_20000.phased_block"/>
401 <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>
402 <element name="output_04.assembly_02.100_20000.phased_block"/>
403 <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>
404 </output_collection>
405 <output_collection name="bed_files" type="list" count="6">
406 <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>
407 <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>
408 <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>
409 <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>
410 <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>
411 <element name="output_04.assembly_02.sort" ftype="bed"/>
412 </output_collection> 301 </output_collection>
413 </test> 302 </test>
414 </tests> 303 </tests>
415 <help><![CDATA[ 304 <help><![CDATA[
416 .. class:: infomark 305 .. class:: infomark