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comparison cutadapt.xml @ 37:944ae523bacb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1973d7e076969910f753bf31adc0cdda2fc1530f
author iuc
date Thu, 21 Mar 2024 10:46:29 +0000
parents 64172f1c1202
children fe74900d6dc7
comparison
equal deleted inserted replaced
36:64172f1c1202 37:944ae523bacb
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