Mercurial > repos > bgruening > mitohifi
comparison mitohifi.xml @ 1:99ddbf037d98 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 59301409d1f555702e346d7b6ba3992a4f336691
author | bgruening |
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date | Wed, 03 May 2023 19:33:09 +0000 |
parents | f6065bc6e428 |
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0:f6065bc6e428 | 1:99ddbf037d98 |
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12 --email '${operation_mode.email}' | 12 --email '${operation_mode.email}' |
13 --outfolder ./ | 13 --outfolder ./ |
14 #if $operation_mode.min_length | 14 #if $operation_mode.min_length |
15 --min_length $operation_mode.min_length | 15 --min_length $operation_mode.min_length |
16 #end if | 16 #end if |
17 $operation_mode.exact_specie | 17 $operation_mode.exact_species |
18 && mv ./*fasta ./reference_genome.fasta | 18 && mv ./*fasta ./reference_genome.fasta |
19 && mv ./*gb ./reference_genome.gb | 19 && mv ./*gb ./reference_genome.gb |
20 #elif $operation_mode.command == 'mitohifi' | 20 #elif $operation_mode.command == 'mitohifi' |
21 ln -s '${operation_mode.reference_genbank}' related_mito.gb | 21 ln -s '${operation_mode.reference_genbank}' related_mito.gb |
22 && ln -s '${operation_mode.reference_fasta}' related_mito.fasta | 22 && ln -s '${operation_mode.reference_fasta}' related_mito.fasta |
23 | 23 |
24 && mitohifi_v2.py | 24 && mitohifi.py |
25 #if $operation_mode.input_option.input == 'pacbio' | 25 #if $operation_mode.input_option.input == 'pacbio' |
26 -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }' | 26 -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }' |
27 -m $operation_mode.input_option.bloom_filter | 27 -m $operation_mode.input_option.bloom_filter |
28 #else | 28 #else |
29 -c '${operation_mode.input_option.input_assembly}' | 29 -c '${operation_mode.input_option.input_assembly}' |
51 <param name="command" type="select" label="Operation type selector" help="Select a type of operation"> | 51 <param name="command" type="select" label="Operation type selector" help="Select a type of operation"> |
52 <option value="find_reference">Find a close-related mitochondrial reference genome</option> | 52 <option value="find_reference">Find a close-related mitochondrial reference genome</option> |
53 <option value="mitohifi">Run MitoHiFi</option> | 53 <option value="mitohifi">Run MitoHiFi</option> |
54 </param> | 54 </param> |
55 <when value="find_reference"> | 55 <when value="find_reference"> |
56 <param argument="--species" type="text" value="" label="Specie name" help="Specie name in binomial nomenclature"> | 56 <param argument="--species" type="text" value="" label="Species name" help="Species name in binomial nomenclature"> |
57 <sanitizer invalid_char=""> | 57 <sanitizer invalid_char=""> |
58 <valid initial="string.letters,string.digits"> | 58 <valid initial="string.letters,string.digits"> |
59 <add value=" "/> | 59 <add value=" "/> |
60 </valid> | 60 </valid> |
61 </sanitizer> | 61 </sanitizer> |
70 </valid> | 70 </valid> |
71 </sanitizer> | 71 </sanitizer> |
72 </param> | 72 </param> |
73 <param argument="--min_length" type="integer" | 73 <param argument="--min_length" type="integer" |
74 min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" /> | 74 min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" /> |
75 <param name="exact_specie" argument="-s" type="boolean" | 75 <param name="exact_species" argument="-s" type="boolean" |
76 truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/> | 76 truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/> |
77 </when> | 77 </when> |
78 <when value="mitohifi"> | 78 <when value="mitohifi"> |
79 <conditional name="input_option"> | 79 <conditional name="input_option"> |
80 <param name="input" type="select" label="Input mode"> | 80 <param name="input" type="select" label="Input mode"> |
151 <filter> operation_mode['command'] == 'mitohifi'</filter> | 151 <filter> operation_mode['command'] == 'mitohifi'</filter> |
152 </data> | 152 </data> |
153 <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)"> | 153 <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)"> |
154 <filter> operation_mode['command'] == 'mitohifi'</filter> | 154 <filter> operation_mode['command'] == 'mitohifi'</filter> |
155 </data> | 155 </data> |
156 <data name="mitogenome_annotation" format="png" from_work_dir="final_mitogenome.annotation.png" label="${tool.name} on ${on_string}: final mitogenome annotation (png)"> | |
157 <filter> operation_mode['command'] == 'mitohifi'</filter> | |
158 </data> | |
159 <data name="mitogenome_coverage" format="png" from_work_dir="final_mitogenome.coverage.png" label="${tool.name} on ${on_string}: final mitogenome coverage (png)"> | |
160 <filter> operation_mode['command'] == 'mitohifi'</filter> | |
161 </data> | |
162 <data name="contigs_stats" format="tsv" from_work_dir="contigs_stats.tsv" label="${tool.name} on ${on_string}: contigs stats (TSV)"> | |
163 <filter> operation_mode['command'] == 'mitohifi'</filter> | |
164 </data> | |
156 <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST"> | 165 <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST"> |
157 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter> | 166 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter> |
158 </data> | 167 </data> |
159 <data name="parsed_blast_all" format="txt" from_work_dir="contigs_filtering/parsed_blast_all.txt" label="${tool.name} on ${on_string}: parsed BLAST (all)"> | 168 <data name="parsed_blast_all" format="txt" from_work_dir="contigs_filtering/parsed_blast_all.txt" label="${tool.name} on ${on_string}: parsed BLAST (all)"> |
160 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter> | 169 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter> |
194 <param name="email" value="kk16@sanger.ac.uk"/> | 203 <param name="email" value="kk16@sanger.ac.uk"/> |
195 <param name="min_length" value="1500"/> | 204 <param name="min_length" value="1500"/> |
196 </conditional> | 205 </conditional> |
197 <output name="fasta_reference" ftype="fasta"> | 206 <output name="fasta_reference" ftype="fasta"> |
198 <assert_contents> | 207 <assert_contents> |
199 <has_size value="15742"/> | 208 <has_size value="15593"/> |
200 <has_line line=">NC_054179.1 Spodoptera exempta mitochondrion, complete genome"/> | 209 <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/> |
201 </assert_contents> | 210 </assert_contents> |
202 </output> | 211 </output> |
203 <output name="genbank_reference" ftype="genbank"> | 212 <output name="genbank_reference" ftype="genbank"> |
204 <assert_contents> | 213 <assert_contents> |
205 <has_size value="43468"/> | 214 <has_size value="43220"/> |
206 <has_line line="DEFINITION Spodoptera exempta mitochondrion, complete genome."/> | 215 <has_line line="DEFINITION Condica capensis mitochondrion, complete genome."/> |
207 </assert_contents> | 216 </assert_contents> |
208 </output> | 217 </output> |
209 </test> | 218 </test> |
210 <!--Test 02--> | 219 <!--Test 02--> |
211 <test expect_num_outputs="5"> | 220 <!--<test expect_num_outputs="8"> |
212 <conditional name="operation_mode"> | 221 <conditional name="operation_mode"> |
213 <param name="command" value="mitohifi"/> | 222 <param name="command" value="mitohifi"/> |
214 <conditional name="input_option"> | 223 <conditional name="input_option"> |
215 <param name="input" value="pacbio"/> | 224 <param name="input" value="pacbio"/> |
216 <param name="input_reads" value="pacbio_01.fasta.gz"/> | 225 <param name="input_reads" value="pacbio_01.fasta.gz"/> |
247 <assert_contents> | 256 <assert_contents> |
248 <has_size value="15329"/> | 257 <has_size value="15329"/> |
249 <has_line line=">ptg000001c"/> | 258 <has_line line=">ptg000001c"/> |
250 </assert_contents> | 259 </assert_contents> |
251 </output> | 260 </output> |
252 </test> | 261 </test>--> |
253 <!--Test 03--> | 262 <!--Test 03--> |
254 <test expect_num_outputs="5"> | 263 <test expect_num_outputs="8"> |
255 <conditional name="operation_mode"> | 264 <conditional name="operation_mode"> |
256 <param name="command" value="mitohifi"/> | 265 <param name="command" value="mitohifi"/> |
257 <conditional name="input_option"> | 266 <conditional name="input_option"> |
258 <param name="input" value="pacbio"/> | 267 <param name="input" value="pacbio"/> |
259 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 268 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
295 <has_line line=">ptg000001c"/> | 304 <has_line line=">ptg000001c"/> |
296 </assert_contents> | 305 </assert_contents> |
297 </output> | 306 </output> |
298 </test> | 307 </test> |
299 <!--Test 04--> | 308 <!--Test 04--> |
300 <test expect_num_outputs="5"> | 309 <test expect_num_outputs="8"> |
301 <conditional name="operation_mode"> | 310 <conditional name="operation_mode"> |
302 <param name="command" value="mitohifi"/> | 311 <param name="command" value="mitohifi"/> |
303 <conditional name="input_option"> | 312 <conditional name="input_option"> |
304 <param name="input" value="pacbio"/> | 313 <param name="input" value="pacbio"/> |
305 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 314 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
341 <has_line line=">ptg000001c"/> | 350 <has_line line=">ptg000001c"/> |
342 </assert_contents> | 351 </assert_contents> |
343 </output> | 352 </output> |
344 </test> | 353 </test> |
345 <!--Test 05--> | 354 <!--Test 05--> |
346 <test expect_num_outputs="5"> | 355 <test expect_num_outputs="8"> |
347 <conditional name="operation_mode"> | 356 <conditional name="operation_mode"> |
348 <param name="command" value="mitohifi"/> | 357 <param name="command" value="mitohifi"/> |
349 <conditional name="input_option"> | 358 <conditional name="input_option"> |
350 <param name='input' value="pacbio"/> | 359 <param name='input' value="pacbio"/> |
351 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 360 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
387 <has_line line=">ptg000001c"/> | 396 <has_line line=">ptg000001c"/> |
388 </assert_contents> | 397 </assert_contents> |
389 </output> | 398 </output> |
390 </test> | 399 </test> |
391 <!--Test 06--> | 400 <!--Test 06--> |
392 <test expect_num_outputs="8"> | 401 <test expect_num_outputs="11"> |
393 <conditional name="operation_mode"> | 402 <conditional name="operation_mode"> |
394 <param name="command" value="mitohifi"/> | 403 <param name="command" value="mitohifi"/> |
395 <conditional name="input_option"> | 404 <conditional name="input_option"> |
396 <param name='input' value="pacbio"/> | 405 <param name='input' value="pacbio"/> |
397 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 406 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
449 <has_line line="ptg000001c"/> | 458 <has_line line="ptg000001c"/> |
450 </assert_contents> | 459 </assert_contents> |
451 </output> | 460 </output> |
452 </test> | 461 </test> |
453 <!--Test 07--> | 462 <!--Test 07--> |
454 <test expect_num_outputs="6"> | 463 <test expect_num_outputs="9"> |
455 <conditional name="operation_mode"> | 464 <conditional name="operation_mode"> |
456 <param name="command" value="mitohifi"/> | 465 <param name="command" value="mitohifi"/> |
457 <conditional name="input_option"> | 466 <conditional name="input_option"> |
458 <param name="input" value="pacbio"/> | 467 <param name="input" value="pacbio"/> |
459 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 468 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
500 <has_size value="28"/> | 509 <has_size value="28"/> |
501 </assert_contents> | 510 </assert_contents> |
502 </output> | 511 </output> |
503 </test> | 512 </test> |
504 <!--Test 08--> | 513 <!--Test 08--> |
505 <test expect_num_outputs="6"> | 514 <test expect_num_outputs="9"> |
506 <conditional name="operation_mode"> | 515 <conditional name="operation_mode"> |
507 <param name="command" value="mitohifi"/> | 516 <param name="command" value="mitohifi"/> |
508 <conditional name="input_option"> | 517 <conditional name="input_option"> |
509 <param name='input' value="pacbio"/> | 518 <param name='input' value="pacbio"/> |
510 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 519 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |
577 <has_line line="DEFINITION NC_016067.1_rc_rotated"/> | 586 <has_line line="DEFINITION NC_016067.1_rc_rotated"/> |
578 </assert_contents> | 587 </assert_contents> |
579 </output> | 588 </output> |
580 </test> | 589 </test> |
581 <!--Test 10--> | 590 <!--Test 10--> |
582 <test expect_num_outputs="6"> | 591 <test expect_num_outputs="9"> |
583 <conditional name="operation_mode"> | 592 <conditional name="operation_mode"> |
584 <param name="command" value="mitohifi"/> | 593 <param name="command" value="mitohifi"/> |
585 <conditional name="input_option"> | 594 <conditional name="input_option"> |
586 <param name="input" value="pacbio"/> | 595 <param name="input" value="pacbio"/> |
587 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | 596 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> |