Mercurial > repos > lparsons > cutadapt
comparison cutadapt.xml @ 37:944ae523bacb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1973d7e076969910f753bf31adc0cdda2fc1530f
author | iuc |
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date | Thu, 21 Mar 2024 10:46:29 +0000 |
parents | 64172f1c1202 |
children | fe74900d6dc7 |
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36:64172f1c1202 | 37:944ae523bacb |
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37 #else | 37 #else |
38 #set input_1 = $library.input_1 | 38 #set input_1 = $library.input_1 |
39 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier)) | 39 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier)) |
40 #end if | 40 #end if |
41 | 41 |
42 #if $input_1.is_of_type("fastq"): | 42 #if $input_1.is_of_type("fastq", "fastq.gz", "fastq.bz2"): |
43 #set ext = ".fq" | 43 #set ext = ".fq" |
44 #else | 44 #else |
45 #set ext = ".fa" | 45 #set ext = ".fa" |
46 #end if | 46 #end if |
47 #if $input_1.ext.endswith(".gz"): | 47 #if $input_1.ext.endswith(".gz"): |
59 #set too_long_output = "too_long_output" + $ext | 59 #set too_long_output = "too_long_output" + $ext |
60 #set untrimmed_output = "untrimmed_output" + $ext | 60 #set untrimmed_output = "untrimmed_output" + $ext |
61 ln -f -s '${input_1}' '$read1' && | 61 ln -f -s '${input_1}' '$read1' && |
62 | 62 |
63 #if $paired: | 63 #if $paired: |
64 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"): | 64 #if $input_2.is_of_type("fastq", "fastq.gz", "fastq.bz2"): |
65 #set ext2 = ".fq.gz" | 65 #set ext2 = ".fq" |
66 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 66 #else |
67 #set ext2 = ".fq.gz" | |
68 #else if $input_2.is_of_type('fasta'): | |
69 #set ext2 = ".fa" | 67 #set ext2 = ".fa" |
70 #else: | 68 #end if |
71 #set ext2 = ".fq" | 69 #if $input_2.ext.endswith(".gz"): |
70 #set ext2=ext2+".gz" | |
71 #elif $input_2.ext.endswith(".bz2") | |
72 #set ext2=ext2+".bz2" | |
72 #end if | 73 #end if |
73 #set read2 = $read2 + $ext2 | 74 #set read2 = $read2 + $ext2 |
74 #set out2 = "out2" + $ext2 | 75 #set out2 = "out2" + $ext2 |
75 #set too_short_paired_output = "too_short_paired_output" + $ext2 | 76 #set too_short_paired_output = "too_short_paired_output" + $ext2 |
76 #set too_long_paired_output = "too_long_paired_output" + $ext2 | 77 #set too_long_paired_output = "too_long_paired_output" + $ext2 |
317 <option value="json_stats">Statistics in JSON format</option> | 318 <option value="json_stats">Statistics in JSON format</option> |
318 </param> | 319 </param> |
319 </inputs> | 320 </inputs> |
320 | 321 |
321 <outputs> | 322 <outputs> |
322 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output"> | 323 <data name="out1" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output"> |
323 <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter> | 324 <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter> |
324 <expand macro="inherit_format_1" /> | 325 <expand macro="inherit_format_1" /> |
325 </data> | 326 </data> |
326 | 327 |
327 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" > | 328 <data name="out2" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" > |
328 <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter> | 329 <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter> |
329 <expand macro="inherit_format_2" /> | 330 <expand macro="inherit_format_2" /> |
330 </data> | 331 </data> |
331 | 332 |
332 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads"> | 333 <collection name="out_pairs" type="paired" format_source="library|input_1" label="${tool.name} on ${on_string}: Reads"> |
333 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter> | 334 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter> |
334 <data name="forward" from_work_dir="out1.*" /> | 335 <data name="forward" from_work_dir="out1.*" /> |
335 <data name="reverse" from_work_dir="out2.*" /> | 336 <data name="reverse" from_work_dir="out2.*" /> |
336 </collection> | 337 </collection> |
337 | 338 |
338 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> | 339 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> |
339 <filter>output_selector and 'report' in output_selector</filter> | 340 <filter>output_selector and 'report' in output_selector</filter> |
340 </data> | 341 </data> |
341 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" > | 342 <data name="info_file" format="txt" metadata_source="library|input_1" label="${tool.name} on ${on_string}: Info File" > |
342 <filter>output_selector and 'info_file' in output_selector</filter> | 343 <filter>output_selector and 'info_file' in output_selector</filter> |
343 </data> | 344 </data> |
344 | 345 |
345 <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" > | 346 <data name="rest_output" format="fastqsanger" metadata_source="library|input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" > |
346 <filter>output_selector and 'rest_file' in output_selector</filter> | 347 <filter>output_selector and 'rest_file' in output_selector</filter> |
347 <expand macro="inherit_format_1" /> | 348 <expand macro="inherit_format_1" /> |
348 </data> | 349 </data> |
349 | 350 |
350 <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" > | 351 <data name="wild_output" format="txt" metadata_source="library|input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" > |
351 <filter>output_selector and 'wildcard_file' in output_selector</filter> | 352 <filter>output_selector and 'wildcard_file' in output_selector</filter> |
352 </data> | 353 </data> |
353 | 354 |
354 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" > | 355 <data name="untrimmed_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" > |
355 <filter>output_selector and 'untrimmed_file' in output_selector</filter> | 356 <filter>output_selector and 'untrimmed_file' in output_selector</filter> |
356 <expand macro="inherit_format_1" /> | 357 <expand macro="inherit_format_1" /> |
357 </data> | 358 </data> |
358 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" > | 359 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" > |
359 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> | 360 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> |
360 <filter>output_selector and 'untrimmed_file' in output_selector </filter> | 361 <filter>output_selector and 'untrimmed_file' in output_selector </filter> |
361 <expand macro="inherit_format_2" /> | 362 <expand macro="inherit_format_2" /> |
362 </data> | 363 </data> |
363 | 364 |
364 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" > | 365 <data name="too_short_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" > |
365 <filter>output_selector and 'too_short_file' in output_selector</filter> | 366 <filter>output_selector and 'too_short_file' in output_selector</filter> |
366 <expand macro="inherit_format_1" /> | 367 <expand macro="inherit_format_1" /> |
367 </data> | 368 </data> |
368 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" > | 369 <data name="too_short_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" > |
369 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> | 370 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> |
370 <filter>output_selector and 'too_short_file' in output_selector</filter> | 371 <filter>output_selector and 'too_short_file' in output_selector</filter> |
371 <expand macro="inherit_format_2" /> | 372 <expand macro="inherit_format_2" /> |
372 </data> | 373 </data> |
373 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" > | 374 <data name="too_long_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" > |
374 <filter>output_selector and 'too_long_file' in output_selector</filter> | 375 <filter>output_selector and 'too_long_file' in output_selector</filter> |
375 <expand macro="inherit_format_1" /> | 376 <expand macro="inherit_format_1" /> |
376 </data> | 377 </data> |
377 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" > | 378 <data name="too_long_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" > |
378 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> | 379 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> |
379 <filter>output_selector and 'too_long_file' in output_selector</filter> | 380 <filter>output_selector and 'too_long_file' in output_selector</filter> |
380 <expand macro="inherit_format_2" /> | 381 <expand macro="inherit_format_2" /> |
381 </data> | 382 </data> |
382 <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" > | 383 <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" > |
1331 <param name="adapter_source_list" value="user"/> | 1332 <param name="adapter_source_list" value="user"/> |
1332 <param name="adapter" value="AGATCGGAAGAGC"/> | 1333 <param name="adapter" value="AGATCGGAAGAGC"/> |
1333 </conditional> | 1334 </conditional> |
1334 </repeat> | 1335 </repeat> |
1335 </section> | 1336 </section> |
1336 <assert_stdout> | 1337 <assert_stderr> |
1337 <has_text text="Reads are improperly paired"/> | 1338 <has_text text="Reads are improperly paired"/> |
1338 </assert_stdout> | 1339 </assert_stderr> |
1339 </test> | 1340 </test> |
1340 </tests> | 1341 </tests> |
1341 | 1342 |
1342 <help><![CDATA[ | 1343 <help><![CDATA[ |
1343 | 1344 |