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comparison semibin.xml @ 1:2eeff5d4a5de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
author iuc
date Mon, 27 Mar 2023 08:22:16 +0000
parents d1f0be443b8b
children 9de6b5e570df
comparison
equal deleted inserted replaced
0:d1f0be443b8b 1:2eeff5d4a5de
108 </collection> 108 </collection>
109 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> 109 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
110 <filter>mode["select"]!="multi"</filter> 110 <filter>mode["select"]!="multi"</filter>
111 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" /> 111 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
112 </collection> 112 </collection>
113 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> 113 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">
114 <filter>mode["select"]=="multi"</filter> 114 <filter>mode["select"]=="multi"</filter>
115 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/bins" /> 115 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/bins" />
116 </collection> 116 </collection>
117 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> 117 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
118 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter> 118 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
156 <param name="batch_size" value="2048"/> 156 <param name="batch_size" value="2048"/>
157 </section> 157 </section>
158 <section name="bin"> 158 <section name="bin">
159 <param name="max_node" value="1"/> 159 <param name="max_node" value="1"/>
160 <param name="max_edges" value="200"/> 160 <param name="max_edges" value="200"/>
161 <param name="minfasta_kbs" value="200"/> 161 <param name="minfasta_kbs" value="2"/>
162 <param name="no_recluster" value="false"/> 162 <param name="no_recluster" value="false"/>
163 </section> 163 </section>
164 <param name="extra_output" value="data,coverage,contigs"/> 164 <param name="extra_output" value="data,coverage,contigs"/>
165 <output_collection name="output_recluster_bins" count="0"/> 165 <output_collection name="output_recluster_bins" count="39">
166 <output_collection name="output_bins" count="3"> 166 <element name="0" ftype="fasta">
167 <element name="0" ftype="fasta">
168 <assert_contents> 167 <assert_contents>
169 <has_text text=">g1k_0"/> 168 <has_text text=">g1k_0"/>
170 </assert_contents> 169 </assert_contents>
171 </element> 170 </element>
172 <element name="1" ftype="fasta"> 171 <element name="1" ftype="fasta">
173 <assert_contents> 172 <assert_contents>
173 <has_text text=">g1k_1"/>
174 </assert_contents>
175 </element>
176 <element name="2" ftype="fasta">
177 <assert_contents>
178 <has_text text=">g1k_2"/>
179 </assert_contents>
180 </element>
181 <element name="39" ftype="fasta">
182 <assert_contents>
183 <has_text text=">g3k_9"/>
184 </assert_contents>
185 </element>
186 </output_collection>
187 <output_collection name="output_bins" count="0">
188 <!--<element name="0" ftype="fasta">
189 <assert_contents>
190 <has_text text=">g1k_0"/>
191 </assert_contents>
192 </element>
193 <element name="1" ftype="fasta">
194 <assert_contents>
174 <has_text text=">g2k_0"/> 195 <has_text text=">g2k_0"/>
175 </assert_contents> 196 </assert_contents>
176 </element> 197 </element>
177 <element name="2" ftype="fasta"> 198 <element name="2" ftype="fasta">
178 <assert_contents> 199 <assert_contents>
179 <has_text text=">g3k_0"/> 200 <has_text text=">g3k_0"/>
180 </assert_contents> 201 </assert_contents>
181 </element> 202 </element>-->
182 </output_collection> 203 </output_collection>
183 <output name="single_data" ftype="csv"> 204 <output name="single_data" ftype="csv">
184 <assert_contents> 205 <assert_contents>
185 <has_text text="g1k_0"/> 206 <has_text text="g1k_0"/>
186 <has_text text="g4k_7"/> 207 <has_text text="g4k_7"/>
290 <has_text text="g2k_7_2"/> 311 <has_text text="g2k_7_2"/>
291 </assert_contents> 312 </assert_contents>
292 </element> 313 </element>
293 </output_collection> 314 </output_collection>
294 </test> 315 </test>
316 <test expect_num_outputs="4">
317 <conditional name="mode">
318 <param name="select" value="co"/>
319 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
320 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
321 <conditional name="ref">
322 <param name="select" value="taxonomy"/>
323 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
324 </conditional>
325 </conditional>
326 <conditional name="min_len">
327 <param name="method" value="ratio"/>
328 <param name="ratio" value="0.05"/>
329 </conditional>
330 <param name="orf_finder" value="fraggenescan"/>
331 <param name="random-seed" value="0"/>
332 <section name="annot">
333 <param name="ml_threshold" value=""/>
334 </section>
335 <section name="training">
336 <param name="epoches" value="20"/>
337 <param name="batch_size" value="2048"/>
338 </section>
339 <section name="bin">
340 <param name="max_node" value="1"/>
341 <param name="max_edges" value="200"/>
342 <param name="minfasta_kbs" value="200"/>
343 <param name="no_recluster" value="false"/>
344 </section>
345 <param name="extra_output" value="coverage"/>
346 <output_collection name="output_recluster_bins" count="1">
347 <element name="30" ftype="fasta">
348 <assert_contents>
349 <has_text text=">g3k_0"/>
350 </assert_contents>
351 </element>
352 </output_collection>
353 <output_collection name="co_cov" count="5">
354 <element name="0" ftype="csv">
355 <assert_contents>
356 <has_text text="g1k_0"/>
357 <has_text text="g2k_7"/>
358 </assert_contents>
359 </element>
360 <element name="1" ftype="csv">
361 <assert_contents>
362 <has_text text="g1k_0"/>
363 <has_text text="g2k_7"/>
364 </assert_contents>
365 </element>
366 <element name="4" ftype="csv">
367 <assert_contents>
368 <has_text text="g1k_0"/>
369 <has_text text="g2k_7"/>
370 </assert_contents>
371 </element>
372 </output_collection>
373 <output_collection name="co_split_cov" count="5">
374 <element name="0" ftype="csv">
375 <assert_contents>
376 <has_text text="g1k_0_1"/>
377 <has_text text="g2k_7_2"/>
378 </assert_contents>
379 </element>
380 <element name="1" ftype="csv">
381 <assert_contents>
382 <has_text text="g1k_0_1"/>
383 <has_text text="g2k_7_2"/>
384 </assert_contents>
385 </element>
386 <element name="2" ftype="csv">
387 <assert_contents>
388 <has_text text="g1k_0_1"/>
389 <has_text text="g2k_7_2"/>
390 </assert_contents>
391 </element>
392 </output_collection>
393 </test>
295 <test expect_num_outputs="1"> 394 <test expect_num_outputs="1">
296 <conditional name="mode"> 395 <conditional name="mode">
297 <param name="select" value="single"/> 396 <param name="select" value="single"/>
298 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 397 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
299 <param name="input_bam" ftype="bam" value="input_single.bam"/> 398 <param name="input_bam" ftype="bam" value="input_single.bam"/>
328 <has_text text=">g1k_0"/> 427 <has_text text=">g1k_0"/>
329 </assert_contents> 428 </assert_contents>
330 </element> 429 </element>
331 </output_collection> 430 </output_collection>
332 </test> 431 </test>
432 <test expect_num_outputs="2">
433 <conditional name="mode">
434 <param name="select" value="single"/>
435 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
436 <param name="input_bam" ftype="bam" value="input_single.bam"/>
437 <conditional name="ref">
438 <param name="db_selector" value="cached"/>
439 <param name="cached_db" value="test-db"/>
440 </conditional>
441 </conditional>
442 <conditional name="min_len">
443 <param name="method" value="ratio"/>
444 <param name="ratio" value="0.05"/>
445 </conditional>
446 <param name="orf_finder" value="fraggenescan"/>
447 <param name="random-seed" value="0"/>
448 <section name="annot">
449 <param name="ml_threshold" value=""/>
450 </section>
451 <section name="training">
452 <param name="epoches" value="20"/>
453 <param name="batch_size" value="2048"/>
454 </section>
455 <section name="bin">
456 <param name="max_node" value="1"/>
457 <param name="max_edges" value="200"/>
458 <param name="minfasta_kbs" value="200"/>
459 <param name="no_recluster" value="false"/>
460 </section>
461 <param name="extra_output" value=""/>
462 <output_collection name="output_recluster_bins" count="1">
463 <element name="30" ftype="fasta">
464 <assert_contents>
465 <has_text text=">g3k_0"/>
466 </assert_contents>
467 </element>
468 </output_collection>
469 </test>
333 <test expect_num_outputs="8"> 470 <test expect_num_outputs="8">
334 <conditional name="mode"> 471 <conditional name="mode">
335 <param name="select" value="multi"/> 472 <param name="select" value="multi"/>
336 <conditional name="multi_fasta"> 473 <conditional name="multi_fasta">
337 <param name="select" value="concatenated"/> 474 <param name="select" value="concatenated"/>
418 <has_text text=">g1k_0"/> 555 <has_text text=">g1k_0"/>
419 </assert_contents> 556 </assert_contents>
420 </element> 557 </element>
421 </output_collection> 558 </output_collection>
422 </test> 559 </test>
560
423 </tests> 561 </tests>
424 <help><![CDATA[ 562 <help><![CDATA[
425 @HELP_HEADER@ 563 @HELP_HEADER@
426 564
427 Inputs 565 Inputs