Mercurial > repos > crs4 > prokka

comparison test-data/out.sqn @ 14:eaee459f3d69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
author iuc
date Wed, 28 Mar 2018 12:38:42 -0400
parents a17498c603ec
children
comparison
equal deleted inserted replaced
13:a17498c603ec 14:eaee459f3d69
15 subtype strain , 15 subtype strain ,
16 subname "strain" } } , 16 subname "strain" } } ,
17 gcode 11 } } } , 17 gcode 11 } } } ,
18 molinfo { 18 molinfo {
19 biomol genomic } , 19 biomol genomic } ,
20 comment "Annotated using prokka 1.12 from 20 comment "Annotated using prokka 1.13 from
21 https://github.com/tseemann/prokka" , 21 https://github.com/tseemann/prokka" ,
22 user { 22 user {
23 type 23 type
24 str "NcbiCleanup" , 24 str "NcbiCleanup" ,
25 data { 25 data {
40 int 3 } , 40 int 3 } ,
41 { 41 {
42 label 42 label
43 str "day" , 43 str "day" ,
44 data 44 data
45 int 21 } , 45 int 27 } ,
46 { 46 {
47 label 47 label
48 str "year" , 48 str "year" ,
49 data 49 data
50 int 2017 } } } , 50 int 2018 } } } ,
51 create-date 51 create-date
52 std { 52 std {
53 year 2017 , 53 year 2018 ,
54 month 3 , 54 month 3 ,
55 day 21 } } , 55 day 27 } } ,
56 inst { 56 inst {
57 repr raw , 57 repr raw ,
58 mol dna , 58 mol dna ,
59 length 350 , 59 length 350 ,
60 seq-data 60 seq-data
73 mod { 73 mod {
74 { 74 {
75 subtype strain , 75 subtype strain ,
76 subname "strain" } } , 76 subname "strain" } } ,
77 gcode 11 } } } , 77 gcode 11 } } } ,
78 comment "Annotated using prokka 1.12 from 78 comment "Annotated using prokka 1.13 from
79 https://github.com/tseemann/prokka" , 79 https://github.com/tseemann/prokka" ,
80 user { 80 user {
81 type 81 type
82 str "NcbiCleanup" , 82 str "NcbiCleanup" ,
83 data { 83 data {
98 int 3 } , 98 int 3 } ,
99 { 99 {
100 label 100 label
101 str "day" , 101 str "day" ,
102 data 102 data
103 int 21 } , 103 int 27 } ,
104 { 104 {
105 label 105 label
106 str "year" , 106 str "year" ,
107 data 107 data
108 int 2017 } } } , 108 int 2018 } } } ,
109 create-date 109 create-date
110 std { 110 std {
111 year 2017 , 111 year 2018 ,
112 month 3 , 112 month 3 ,
113 day 21 } } , 113 day 27 } } ,
114 seq-set { 114 seq-set {
115 seq { 115 seq {
116 id { 116 id {
117 local 117 local
118 str "contig2" } , 118 str "contig2" } ,
139 seq { 139 seq {
140 id { 140 id {
141 local 141 local
142 str "contig2_1" } , 142 str "contig2_1" } ,
143 descr { 143 descr {
144 title "hypothetical protein PROKKA_00001 [Genus species]" , 144 title "hypothetical protein HMJLFLJH_00001 [Genus species]" ,
145 molinfo { 145 molinfo {
146 biomol peptide , 146 biomol peptide ,
147 tech concept-trans } } , 147 tech concept-trans } } ,
148 inst { 148 inst {
149 repr raw , 149 repr raw ,
175 seq { 175 seq {
176 id { 176 id {
177 local 177 local
178 str "contig2_2" } , 178 str "contig2_2" } ,
179 descr { 179 descr {
180 title "hypothetical protein PROKKA_00002 [Genus species]" , 180 title "hypothetical protein HMJLFLJH_00002 [Genus species]" ,
181 molinfo { 181 molinfo {
182 biomol peptide , 182 biomol peptide ,
183 tech concept-trans } } , 183 tech concept-trans } } ,
184 inst { 184 inst {
185 repr raw , 185 repr raw ,
237 val "ab initio prediction:Prodigal:2.6" } } , 237 val "ab initio prediction:Prodigal:2.6" } } ,
238 xref { 238 xref {
239 { 239 {
240 data 240 data
241 gene { 241 gene {
242 locus-tag "PROKKA_00001" } } } } , 242 locus-tag "HMJLFLJH_00001" } } } } ,
243 { 243 {
244 id 244 id
245 local 245 local
246 id 2 , 246 id 2 ,
247 data 247 data
267 val "ab initio prediction:Prodigal:2.6" } } , 267 val "ab initio prediction:Prodigal:2.6" } } ,
268 xref { 268 xref {
269 { 269 {
270 data 270 data
271 gene { 271 gene {
272 locus-tag "PROKKA_00002" } } } } } } } } , 272 locus-tag "HMJLFLJH_00002" } } } } } } } } ,
273 seq { 273 seq {
274 id { 274 id {
275 local 275 local
276 str "contig3" } , 276 str "contig3" } ,
277 descr { 277 descr {
284 subtype strain , 284 subtype strain ,
285 subname "strain" } } , 285 subname "strain" } } ,
286 gcode 11 } } } , 286 gcode 11 } } } ,
287 molinfo { 287 molinfo {
288 biomol genomic } , 288 biomol genomic } ,
289 comment "Annotated using prokka 1.12 from 289 comment "Annotated using prokka 1.13 from
290 https://github.com/tseemann/prokka" , 290 https://github.com/tseemann/prokka" ,
291 user { 291 user {
292 type 292 type
293 str "NcbiCleanup" , 293 str "NcbiCleanup" ,
294 data { 294 data {
309 int 3 } , 309 int 3 } ,
310 { 310 {
311 label 311 label
312 str "day" , 312 str "day" ,
313 data 313 data
314 int 21 } , 314 int 27 } ,
315 { 315 {
316 label 316 label
317 str "year" , 317 str "year" ,
318 data 318 data
319 int 2017 } } } , 319 int 2018 } } } ,
320 create-date 320 create-date
321 std { 321 std {
322 year 2017 , 322 year 2018 ,
323 month 3 , 323 month 3 ,
324 day 21 } } , 324 day 27 } } ,
325 inst { 325 inst {
326 repr raw , 326 repr raw ,
327 mol dna , 327 mol dna ,
328 length 210 , 328 length 210 ,
329 seq-data 329 seq-data
340 mod { 340 mod {
341 { 341 {
342 subtype strain , 342 subtype strain ,
343 subname "strain" } } , 343 subname "strain" } } ,
344 gcode 11 } } } , 344 gcode 11 } } } ,
345 comment "Annotated using prokka 1.12 from 345 comment "Annotated using prokka 1.13 from
346 https://github.com/tseemann/prokka" , 346 https://github.com/tseemann/prokka" ,
347 user { 347 user {
348 type 348 type
349 str "NcbiCleanup" , 349 str "NcbiCleanup" ,
350 data { 350 data {
365 int 3 } , 365 int 3 } ,
366 { 366 {
367 label 367 label
368 str "day" , 368 str "day" ,
369 data 369 data
370 int 21 } , 370 int 27 } ,
371 { 371 {
372 label 372 label
373 str "year" , 373 str "year" ,
374 data 374 data
375 int 2017 } } } , 375 int 2018 } } } ,
376 create-date 376 create-date
377 std { 377 std {
378 year 2017 , 378 year 2018 ,
379 month 3 , 379 month 3 ,
380 day 21 } } , 380 day 27 } } ,
381 seq-set { 381 seq-set {
382 seq { 382 seq {
383 id { 383 id {
384 local 384 local
385 str "contig4" } , 385 str "contig4" } ,
411 seq { 411 seq {
412 id { 412 id {
413 local 413 local
414 str "contig4_1" } , 414 str "contig4_1" } ,
415 descr { 415 descr {
416 title "hypothetical protein PROKKA_00003 [Genus species]" , 416 title "hypothetical protein HMJLFLJH_00003 [Genus species]" ,
417 molinfo { 417 molinfo {
418 biomol peptide , 418 biomol peptide ,
419 tech concept-trans } } , 419 tech concept-trans } } ,
420 inst { 420 inst {
421 repr raw , 421 repr raw ,
476 val "ab initio prediction:Prodigal:2.6" } } , 476 val "ab initio prediction:Prodigal:2.6" } } ,
477 xref { 477 xref {
478 { 478 {
479 data 479 data
480 gene { 480 gene {
481 locus-tag "PROKKA_00003" } } } } } } } } , 481 locus-tag "HMJLFLJH_00003" } } } } } } } } ,
482 set { 482 set {
483 class nuc-prot , 483 class nuc-prot ,
484 descr { 484 descr {
485 source { 485 source {
486 org { 486 org {
489 mod { 489 mod {
490 { 490 {
491 subtype strain , 491 subtype strain ,
492 subname "strain" } } , 492 subname "strain" } } ,
493 gcode 11 } } } , 493 gcode 11 } } } ,
494 comment "Annotated using prokka 1.12 from 494 comment "Annotated using prokka 1.13 from
495 https://github.com/tseemann/prokka" , 495 https://github.com/tseemann/prokka" ,
496 user { 496 user {
497 type 497 type
498 str "NcbiCleanup" , 498 str "NcbiCleanup" ,
499 data { 499 data {
514 int 3 } , 514 int 3 } ,
515 { 515 {
516 label 516 label
517 str "day" , 517 str "day" ,
518 data 518 data
519 int 21 } , 519 int 27 } ,
520 { 520 {
521 label 521 label
522 str "year" , 522 str "year" ,
523 data 523 data
524 int 2017 } } } , 524 int 2018 } } } ,
525 create-date 525 create-date
526 std { 526 std {
527 year 2017 , 527 year 2018 ,
528 month 3 , 528 month 3 ,
529 day 21 } } , 529 day 27 } } ,
530 seq-set { 530 seq-set {
531 seq { 531 seq {
532 id { 532 id {
533 local 533 local
534 str "contig5" } , 534 str "contig5" } ,
550 seq { 550 seq {
551 id { 551 id {
552 local 552 local
553 str "contig5_1" } , 553 str "contig5_1" } ,
554 descr { 554 descr {
555 title "hypothetical protein PROKKA_00004 [Genus species]" , 555 title "hypothetical protein HMJLFLJH_00004 [Genus species]" ,
556 molinfo { 556 molinfo {
557 biomol peptide , 557 biomol peptide ,
558 tech concept-trans } } , 558 tech concept-trans } } ,
559 inst { 559 inst {
560 repr raw , 560 repr raw ,
612 val "ab initio prediction:Prodigal:2.6" } } , 612 val "ab initio prediction:Prodigal:2.6" } } ,
613 xref { 613 xref {
614 { 614 {
615 data 615 data
616 gene { 616 gene {
617 locus-tag "PROKKA_00004" } } } } } } } } , 617 locus-tag "HMJLFLJH_00004" } } } } } } } } ,
618 set { 618 set {
619 class nuc-prot , 619 class nuc-prot ,
620 descr { 620 descr {
621 source { 621 source {
622 org { 622 org {
625 mod { 625 mod {
626 { 626 {
627 subtype strain , 627 subtype strain ,
628 subname "strain" } } , 628 subname "strain" } } ,
629 gcode 11 } } } , 629 gcode 11 } } } ,
630 comment "Annotated using prokka 1.12 from 630 comment "Annotated using prokka 1.13 from
631 https://github.com/tseemann/prokka" , 631 https://github.com/tseemann/prokka" ,
632 user { 632 user {
633 type 633 type
634 str "NcbiCleanup" , 634 str "NcbiCleanup" ,
635 data { 635 data {
650 int 3 } , 650 int 3 } ,
651 { 651 {
652 label 652 label
653 str "day" , 653 str "day" ,
654 data 654 data
655 int 21 } , 655 int 27 } ,
656 { 656 {
657 label 657 label
658 str "year" , 658 str "year" ,
659 data 659 data
660 int 2017 } } } , 660 int 2018 } } } ,
661 create-date 661 create-date
662 std { 662 std {
663 year 2017 , 663 year 2018 ,
664 month 3 , 664 month 3 ,
665 day 21 } } , 665 day 27 } } ,
666 seq-set { 666 seq-set {
667 seq { 667 seq {
668 id { 668 id {
669 local 669 local
670 str "contig6" } , 670 str "contig6" } ,
705 seq { 705 seq {
706 id { 706 id {
707 local 707 local
708 str "contig6_1" } , 708 str "contig6_1" } ,
709 descr { 709 descr {
710 title "hypothetical protein PROKKA_00005 [Genus species]" , 710 title "hypothetical protein HMJLFLJH_00005 [Genus species]" ,
711 molinfo { 711 molinfo {
712 biomol peptide , 712 biomol peptide ,
713 tech concept-trans } } , 713 tech concept-trans } } ,
714 inst { 714 inst {
715 repr raw , 715 repr raw ,
770 val "ab initio prediction:Prodigal:2.6" } } , 770 val "ab initio prediction:Prodigal:2.6" } } ,
771 xref { 771 xref {
772 { 772 {
773 data 773 data
774 gene { 774 gene {
775 locus-tag "PROKKA_00005" } } } } } } } } , 775 locus-tag "HMJLFLJH_00005" } } } } } } } } ,
776 seq { 776 seq {
777 id { 777 id {
778 local 778 local
779 str "contig7" } , 779 str "contig7" } ,
780 descr { 780 descr {
787 subtype strain , 787 subtype strain ,
788 subname "strain" } } , 788 subname "strain" } } ,
789 gcode 11 } } } , 789 gcode 11 } } } ,
790 molinfo { 790 molinfo {
791 biomol genomic } , 791 biomol genomic } ,
792 comment "Annotated using prokka 1.12 from 792 comment "Annotated using prokka 1.13 from
793 https://github.com/tseemann/prokka" , 793 https://github.com/tseemann/prokka" ,
794 user { 794 user {
795 type 795 type
796 str "NcbiCleanup" , 796 str "NcbiCleanup" ,
797 data { 797 data {
812 int 3 } , 812 int 3 } ,
813 { 813 {
814 label 814 label
815 str "day" , 815 str "day" ,
816 data 816 data
817 int 21 } , 817 int 27 } ,
818 { 818 {
819 label 819 label
820 str "year" , 820 str "year" ,
821 data 821 data
822 int 2017 } } } , 822 int 2018 } } } ,
823 create-date 823 create-date
824 std { 824 std {
825 year 2017 , 825 year 2018 ,
826 month 3 , 826 month 3 ,
827 day 21 } } , 827 day 27 } } ,
828 inst { 828 inst {
829 repr raw , 829 repr raw ,
830 mol dna , 830 mol dna ,
831 length 276 , 831 length 276 ,
832 seq-data 832 seq-data