Mercurial > repos > artbio > concatenate_multiple_datasets
comparison catWrapper.xml @ 8:5b2cc63d7a21 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
author | artbio |
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date | Fri, 13 Oct 2023 09:46:58 +0000 |
parents | 55cf9d9defd1 |
children | 5b1b635232ed |
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7:55cf9d9defd1 | 8:5b2cc63d7a21 |
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1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1"> | 1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.2"> |
2 <description>tail-to-head by specifying how</description> | 2 <description>tail-to-head while specifying how</description> |
3 <command><![CDATA[ | 3 <command><![CDATA[ |
4 #if $headers == 0: | 4 #if $headers == 0: |
5 #set $concat_command = "cat" | 5 #set $concat_command = "cat" |
6 #else: | 6 #else: |
7 #set $concat_command = 'tail -q -n +'+ str(int($headers)+1) | 7 #set $concat_command = 'tail -q -n +'+ str(int($headers)+1) |
231 <option value="simple_collections">2 Collections</option> | 231 <option value="simple_collections">2 Collections</option> |
232 <option value="paired_collection">Paired collection</option> | 232 <option value="paired_collection">Paired collection</option> |
233 <option value="nested_collection">Nested collection</option> | 233 <option value="nested_collection">Nested collection</option> |
234 </param> | 234 </param> |
235 <when value="singles"> | 235 <when value="singles"> |
236 <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/> | 236 <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" format="fastq,fastq.gz,txt,tabular,bed" |
237 help="All inputed datasets will be concatenated tail-to-head."/> | |
237 </when> | 238 </when> |
238 <when value="paired_collection"> | 239 <when value="paired_collection"> |
239 <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collection to concatenate"/> | 240 <param name="inputs" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,txt,tabular,bed" |
241 label="Input paired collection to concatenate"/> | |
240 <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?"> | 242 <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?"> |
241 <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option> | 243 <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option> |
242 <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option> | 244 <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option> |
243 <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option> | 245 <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option> |
244 </param> | 246 </param> |
260 </data> | 262 </data> |
261 <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true"> | 263 <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true"> |
262 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter> | 264 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter> |
263 </data> | 265 </data> |
264 <collection name="paired_output" type="paired" label="Concatenation by strtand"> | 266 <collection name="paired_output" type="paired" label="Concatenation by strtand"> |
265 <discover_datasets pattern="(?P<name>.*)\.listed\.(?P<ext>.*)\.listed" visible="false" directory="concatenated"/> | 267 <discover_datasets pattern="(?P<name>.*)\.listed\.(?P<ext>.*)\.listed" format="fastq" visible="false" directory="concatenated"/> |
266 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter> | 268 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter> |
267 </collection> | 269 </collection> |
268 <collection name="list_output" type="list" label="Concatenation by pairs"> | 270 <collection name="list_output" type="list" label="Concatenation by pairs"> |
269 <discover_datasets pattern="(?P<identifier_0>.*)\.listed\.(?P<ext>.*)\.listed" visible="false" directory="concatenated"/> | 271 <discover_datasets pattern="(?P<identifier_0>.*)\.listed\.(?P<ext>.*)\.listed" format="fastq" visible="false" directory="concatenated"/> |
270 <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter> | 272 <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter> |
271 </collection> | 273 </collection> |
272 </outputs> | 274 </outputs> |
273 <tests> | 275 <tests> |
274 <!-- Single files concatenation --> | 276 <!-- Single files concatenation --> |
275 <test> <!-- Test 2 single files concatenation with no other option --> | 277 <test expect_num_outputs="1"> <!-- Test 1 single files concatenation with no other option --> |
276 <param name="input_type" value="singles" /> | 278 <param name="input_type" value="singles" /> |
277 <param name="inputs" value="1.bed,2.bed"/> | 279 <param name="inputs" value="1.bed,2.bed"/> |
278 <param name="dataset_names" value="No" /> | 280 <param name="dataset_names" value="No" /> |
279 <param name="headers" value="0" /> | 281 <param name="headers" value="0" /> |
280 <output name="out_file1" file="cat_wrapper_out1.bed"/> | 282 <output name="out_file1" file="cat_wrapper_out1.bed"/> |
281 </test> | 283 </test> |
282 <test> <!-- Test 2 single files concatenation with dataset names activated --> | 284 <test expect_num_outputs="1"> <!-- Test 2 single files concatenation with dataset names activated --> |
283 <param name="input_type" value="singles" /> | 285 <param name="input_type" value="singles" /> |
284 <param name="inputs" value="1.bed,2.bed"/> | 286 <param name="inputs" value="1.bed,2.bed"/> |
285 <param name="dataset_names" value="Yes" /> | 287 <param name="dataset_names" value="Yes" /> |
286 <param name="headers" value="0" /> | 288 <param name="headers" value="0" /> |
287 <output name="out_file1" file="cat_wrapper_out2.bed"/> | 289 <output name="out_file1" file="cat_wrapper_out2.bed"/> |
288 </test> | 290 </test> |
289 <test> <!-- Test 2 single files concatenation skipping 1 line --> | 291 <test expect_num_outputs="1"> <!-- Test 3 single files concatenation skipping 1 line --> |
290 <param name="input_type" value="singles" /> | 292 <param name="input_type" value="singles" /> |
291 <param name="inputs" value="1.bed,2.bed"/> | 293 <param name="inputs" value="1.bed,2.bed"/> |
292 <param name="dataset_names" value="No" /> | 294 <param name="dataset_names" value="No" /> |
293 <param name="headers" value="1" /> | 295 <param name="headers" value="1" /> |
294 <output name="out_file1" file="cat_wrapper_out3.bed"/> | 296 <output name="out_file1" file="cat_wrapper_out3.bed"/> |
295 </test> | 297 </test> |
296 <test> <!-- Test gz handling with no options --> | 298 <test expect_num_outputs="1"> <!-- Test 4 gz handling with no options --> |
297 <param name="input_type" value="singles" /> | 299 <param name="input_type" value="singles" /> |
298 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> | 300 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> |
299 <param name="dataset_names" value="No" /> | 301 <param name="dataset_names" value="No" /> |
300 <param name="headers" value="0" /> | 302 <param name="headers" value="0" /> |
301 <output name="out_file1" file="1.fastq.gz" decompress="True"/> | 303 <output name="out_file1" file="1.fastq.gz" decompress="True"/> |
302 </test> | 304 </test> |
303 <test> <!-- Test gz handling with options --> | 305 <test expect_num_outputs="1"> <!-- Test 5 gz handling with options --> |
304 <param name="input_type" value="singles" /> | 306 <param name="input_type" value="singles" /> |
305 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> | 307 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> |
306 <param name="dataset_names" value="Yes" /> | 308 <param name="dataset_names" value="Yes" /> |
307 <param name="headers" value="4" /> | 309 <param name="headers" value="4" /> |
308 <output name="out_file1" file="1_options.fastq.gz" decompress="True"/> | 310 <output name="out_file1" file="1_options.fastq.gz" decompress="True"/> |
309 </test> | 311 </test> |
310 <!-- Test paired options --> | 312 <!-- Test paired options --> |
311 <test> <!-- Test paired collection concatenation by_pair with no other option --> | 313 <test expect_num_outputs="1"> <!-- Test 6 paired collection concatenation by_pair with no other option --> |
312 <param name="input_type" value="paired_collection" /> | 314 <param name="input_type" value="paired_collection" /> |
313 <param name="paired_cat_type" value="by_pair"/> | 315 <param name="paired_cat_type" value="by_pair"/> |
314 <param name="inputs"> | 316 <param name="inputs"> |
315 <collection type="list:paired"> | 317 <collection type="list:paired"> |
316 <element name="2"> | 318 <element name="2"> |
339 <element name="2" file="2.fastq"/> | 341 <element name="2" file="2.fastq"/> |
340 <element name="3" file="3.fastq"/> | 342 <element name="3" file="3.fastq"/> |
341 <element name="4" file="4.fastq"/> | 343 <element name="4" file="4.fastq"/> |
342 </output_collection> | 344 </output_collection> |
343 </test> | 345 </test> |
344 <test> <!-- Test paired collection concatenation by_strand with no other option --> | 346 <test expect_num_outputs="1"> <!-- Test 7 paired collection concatenation by_strand with no other option --> |
345 <param name="input_type" value="paired_collection" /> | 347 <param name="input_type" value="paired_collection" /> |
346 <param name="paired_cat_type" value="by_strand"/> | 348 <param name="paired_cat_type" value="by_strand"/> |
347 <param name="inputs"> | 349 <param name="inputs"> |
348 <collection type="list:paired"> | 350 <collection type="list:paired"> |
349 <element name="2"> | 351 <element name="2"> |
371 <output_collection name="paired_output" type="paired" > | 373 <output_collection name="paired_output" type="paired" > |
372 <element name="forward" file="f.fastq"/> | 374 <element name="forward" file="f.fastq"/> |
373 <element name="reverse" file="r.fastq"/> | 375 <element name="reverse" file="r.fastq"/> |
374 </output_collection> | 376 </output_collection> |
375 </test> | 377 </test> |
376 <test> <!-- Test 2 collections concatenation --> | 378 <test expect_num_outputs="1"> <!-- Test 8 - 2 collections concatenation --> |
377 <param name="input_type" value="simple_collections" /> | 379 <param name="input_type" value="simple_collections" /> |
378 <param name="collection_cat_type" value="two_collections"/> | |
379 <param name="input_1"> | 380 <param name="input_1"> |
380 <collection type="list"> | 381 <collection type="list"> |
381 <element name="2" value="2_f.fastq"/> | 382 <element name="2" value="2_f.fastq"/> |
382 <element name="3" value="3_f.fastq"/> | 383 <element name="3" value="3_f.fastq"/> |
383 <element name="4" value="4_f.fastq"/> | 384 <element name="4" value="4_f.fastq"/> |
396 <element name="2" file="2.fastq"/> | 397 <element name="2" file="2.fastq"/> |
397 <element name="3" file="3.fastq"/> | 398 <element name="3" file="3.fastq"/> |
398 <element name="4" file="4.fastq"/> | 399 <element name="4" file="4.fastq"/> |
399 </output_collection> | 400 </output_collection> |
400 </test> | 401 </test> |
401 <test> <!-- Test 2 collections concatenation with other options--> | 402 <test expect_num_outputs="1"> <!-- Test 9 - 2 collections concatenation with other options--> |
402 <param name="input_type" value="simple_collections" /> | 403 <param name="input_type" value="simple_collections" /> |
403 <param name="collection_cat_type" value="two_collections"/> | |
404 <param name="input_1"> | 404 <param name="input_1"> |
405 <collection type="list"> | 405 <collection type="list"> |
406 <element name="1_f.fastq.gz" value="1_f.fastq.gz"/> | 406 <element name="1_f.fastq.gz" value="1_f.fastq.gz"/> |
407 </collection> | 407 </collection> |
408 </param> | 408 </param> |
415 <param name="headers" value="4" /> | 415 <param name="headers" value="4" /> |
416 <output_collection name="list_output" type="list" count="1" > | 416 <output_collection name="list_output" type="list" count="1" > |
417 <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/> | 417 <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/> |
418 </output_collection> | 418 </output_collection> |
419 </test> | 419 </test> |
420 <test> <!-- Test nested collections concatenation --> | 420 <test expect_num_outputs="1"> <!-- Test 10 nested collections concatenation --> |
421 <param name="input_type" value="nested_collection" /> | 421 <param name="input_type" value="nested_collection" /> |
422 <param name="inputs"> | 422 <param name="inputs"> |
423 <collection type="list:list"> | 423 <collection type="list:list"> |
424 <element name="2"> | 424 <element name="2"> |
425 <collection type="list"> | 425 <collection type="list"> |
439 <output_collection name="list_output" type="list" count="2" > | 439 <output_collection name="list_output" type="list" count="2" > |
440 <element name="2" file="2.fastq"/> | 440 <element name="2" file="2.fastq"/> |
441 <element name="3" file="3.fastq"/> | 441 <element name="3" file="3.fastq"/> |
442 </output_collection> | 442 </output_collection> |
443 </test> | 443 </test> |
444 <test> <!-- Test nested collections concatenation with options and gzip--> | 444 <test expect_num_outputs="1"> <!-- Test 11 nested collections concatenation with options and gzip--> |
445 <param name="input_type" value="nested_collection" /> | 445 <param name="input_type" value="nested_collection" /> |
446 <param name="inputs"> | 446 <param name="inputs"> |
447 <collection type="list:list"> | 447 <collection type="list:list"> |
448 <element name="1"> | 448 <element name="1"> |
449 <collection type="list"> | 449 <collection type="list"> |
670 ----- | 670 ----- |
671 | 671 |
672 Adapted from galaxy's catWrapper.xml to allow multiple input files. | 672 Adapted from galaxy's catWrapper.xml to allow multiple input files. |
673 | 673 |
674 </help> | 674 </help> |
675 <citations> | |
676 <citation type="doi">10.1186/gb-2010-11-8-r86</citation> | |
677 </citations> | |
675 </tool> | 678 </tool> |