# HG changeset patch # User iuc # Date 1522255122 14400 # Node ID eaee459f3d698e5693adf683b627ec3e41c4d4b3 # Parent a17498c603ec26f03e9e73caac60d373b71f9df1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f diff -r a17498c603ec -r eaee459f3d69 prokka.xml --- a/prokka.xml Tue Mar 21 10:13:06 2017 -0400 +++ b/prokka.xml Wed Mar 28 12:38:42 2018 -0400 @@ -1,14 +1,11 @@ - - prokaryotic genome annotation + + Prokaryotic genome annotation - prokka + prokka - - - - + prokka --version - - + @@ -139,6 +136,7 @@ + @@ -169,6 +167,9 @@ outputs and 'tbl' in outputs + + outputs and 'tsv' in outputs + outputs and 'err' in outputs @@ -180,7 +181,7 @@ - + @@ -189,6 +190,7 @@ + @@ -211,7 +213,7 @@ **License and citation** -This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _Earlham Institute: http://earlham.ac.uk/ diff -r a17498c603ec -r eaee459f3d69 test-data/out.err --- a/test-data/out.err Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.err Wed Mar 28 12:38:42 2018 -0400 @@ -47,19 +47,19 @@ DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations. DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig2:40-498 PROKKA_00001 +outdir/prokka:CDS hypothetical protein contig2:40-498 HMJLFLJH_00001 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig2:498-614 PROKKA_00002 +outdir/prokka:CDS hypothetical protein contig2:498-614 HMJLFLJH_00002 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig4:21-884 PROKKA_00003 +outdir/prokka:CDS hypothetical protein contig4:21-884 HMJLFLJH_00003 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig5:275-406 PROKKA_00004 +outdir/prokka:CDS hypothetical protein contig5:275-406 HMJLFLJH_00004 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig6:6-767 PROKKA_00005 +outdir/prokka:CDS hypothetical protein contig6:6-767 HMJLFLJH_00005 DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features outdir/prokka:contig1 (length 350) @@ -69,13 +69,13 @@ DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences. DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same) -outdir/prokka:contig1:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig2:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig3:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig4:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig5:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig6:Annotated using prokka 1.12 from https://github.com/tseemann/prokka -outdir/prokka:contig7:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig1:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig2:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig3:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig4:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig5:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig6:Annotated using prokka 1.13 from https://github.com/tseemann/prokka +outdir/prokka:contig7:Annotated using prokka 1.13 from https://github.com/tseemann/prokka DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa. outdir/prokka:contig2_2 (length 38) diff -r a17498c603ec -r eaee459f3d69 test-data/out.faa --- a/test-data/out.faa Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.faa Wed Mar 28 12:38:42 2018 -0400 @@ -1,18 +1,18 @@ ->PROKKA_00001 hypothetical protein +>HMJLFLJH_00001 hypothetical protein MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM ->PROKKA_00002 hypothetical protein +>HMJLFLJH_00002 hypothetical protein MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF ->PROKKA_00003 hypothetical protein +>HMJLFLJH_00003 hypothetical protein MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS ->PROKKA_00004 hypothetical protein +>HMJLFLJH_00004 hypothetical protein MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL ->PROKKA_00005 hypothetical protein +>HMJLFLJH_00005 hypothetical protein MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV diff -r a17498c603ec -r eaee459f3d69 test-data/out.ffn --- a/test-data/out.ffn Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.ffn Wed Mar 28 12:38:42 2018 -0400 @@ -1,4 +1,4 @@ ->PROKKA_00001 hypothetical protein +>HMJLFLJH_00001 hypothetical protein ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT @@ -7,10 +7,10 @@ GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA ->PROKKA_00002 hypothetical protein +>HMJLFLJH_00002 hypothetical protein ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA ->PROKKA_00003 hypothetical protein +>HMJLFLJH_00003 hypothetical protein ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT @@ -26,11 +26,11 @@ CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT CGCGATTCAATCATGACTTCGTGA ->PROKKA_00004 hypothetical protein +>HMJLFLJH_00004 hypothetical protein TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA ACAATACTGTAG ->PROKKA_00005 hypothetical protein +>HMJLFLJH_00005 hypothetical protein ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT diff -r a17498c603ec -r eaee459f3d69 test-data/out.gbk --- a/test-data/out.gbk Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.gbk Wed Mar 28 12:38:42 2018 -0400 @@ -1,4 +1,4 @@ -LOCUS contig1 350 bp DNA linear 21-MAR-2017 +LOCUS contig1 350 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -6,7 +6,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..350 @@ -21,7 +21,7 @@ 241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt 301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc // -LOCUS contig2 840 bp DNA linear 21-MAR-2017 +LOCUS contig2 840 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -29,7 +29,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..840 @@ -37,7 +37,7 @@ /mol_type="genomic DNA" /strain="strain" CDS 40..498 - /locus_tag="PROKKA_00001" + /locus_tag="HMJLFLJH_00001" /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 @@ -46,7 +46,7 @@ ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM" CDS 498..614 - /locus_tag="PROKKA_00002" + /locus_tag="HMJLFLJH_00002" /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 @@ -68,7 +68,7 @@ 721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga 781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta // -LOCUS contig3 210 bp DNA linear 21-MAR-2017 +LOCUS contig3 210 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -76,7 +76,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..210 @@ -89,7 +89,7 @@ 121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt 181 tgtttcaggg ttatttgaat atctataaca // -LOCUS contig4 1260 bp DNA linear 21-MAR-2017 +LOCUS contig4 1260 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -97,7 +97,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..1260 @@ -105,7 +105,7 @@ /mol_type="genomic DNA" /strain="strain" CDS 21..884 - /locus_tag="PROKKA_00003" + /locus_tag="HMJLFLJH_00003" /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 @@ -139,7 +139,7 @@ 1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc 1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc // -LOCUS contig5 490 bp DNA linear 21-MAR-2017 +LOCUS contig5 490 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -147,7 +147,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..490 @@ -155,7 +155,7 @@ /mol_type="genomic DNA" /strain="strain" CDS 275..406 - /locus_tag="PROKKA_00004" + /locus_tag="HMJLFLJH_00004" /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 @@ -172,7 +172,7 @@ 421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt 481 tttgtttctg // -LOCUS contig6 1960 bp DNA linear 21-MAR-2017 +LOCUS contig6 1960 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -180,7 +180,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..1960 @@ -188,7 +188,7 @@ /mol_type="genomic DNA" /strain="strain" CDS 6..767 - /locus_tag="PROKKA_00005" + /locus_tag="HMJLFLJH_00005" /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 @@ -233,7 +233,7 @@ 1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta 1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact // -LOCUS contig7 276 bp DNA linear 21-MAR-2017 +LOCUS contig7 276 bp DNA linear 27-MAR-2018 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -241,7 +241,7 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.12 from +COMMENT Annotated using prokka 1.13 from https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..276 diff -r a17498c603ec -r eaee459f3d69 test-data/out.gff --- a/test-data/out.gff Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.gff Wed Mar 28 12:38:42 2018 -0400 @@ -6,11 +6,11 @@ ##sequence-region contig5 1 490 ##sequence-region contig6 1 1960 ##sequence-region contig7 1 276 -contig2 Prodigal:2.6 CDS 40 498 . + 0 ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00001;product=hypothetical protein -contig2 Prodigal:2.6 CDS 498 614 . + 0 ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00002;product=hypothetical protein -contig4 Prodigal:2.6 CDS 21 884 . + 0 ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00003;product=hypothetical protein -contig5 Prodigal:2.6 CDS 275 406 . + 0 ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00004;product=hypothetical protein -contig6 Prodigal:2.6 CDS 6 767 . + 0 ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00005;product=hypothetical protein +contig2 Prodigal:2.6 CDS 40 498 . + 0 ID=HMJLFLJH_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=HMJLFLJH_00001;product=hypothetical protein +contig2 Prodigal:2.6 CDS 498 614 . + 0 ID=HMJLFLJH_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=HMJLFLJH_00002;product=hypothetical protein +contig4 Prodigal:2.6 CDS 21 884 . + 0 ID=HMJLFLJH_00003;inference=ab initio prediction:Prodigal:2.6;locus_tag=HMJLFLJH_00003;product=hypothetical protein +contig5 Prodigal:2.6 CDS 275 406 . + 0 ID=HMJLFLJH_00004;inference=ab initio prediction:Prodigal:2.6;locus_tag=HMJLFLJH_00004;product=hypothetical protein +contig6 Prodigal:2.6 CDS 6 767 . + 0 ID=HMJLFLJH_00005;inference=ab initio prediction:Prodigal:2.6;locus_tag=HMJLFLJH_00005;product=hypothetical protein ##FASTA >contig1 GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA diff -r a17498c603ec -r eaee459f3d69 test-data/out.sqn --- a/test-data/out.sqn Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.sqn Wed Mar 28 12:38:42 2018 -0400 @@ -17,7 +17,7 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -42,17 +42,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , inst { repr raw , mol dna , @@ -75,7 +75,7 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -100,17 +100,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , seq-set { seq { id { @@ -141,7 +141,7 @@ local str "contig2_1" } , descr { - title "hypothetical protein PROKKA_00001 [Genus species]" , + title "hypothetical protein HMJLFLJH_00001 [Genus species]" , molinfo { biomol peptide , tech concept-trans } } , @@ -177,7 +177,7 @@ local str "contig2_2" } , descr { - title "hypothetical protein PROKKA_00002 [Genus species]" , + title "hypothetical protein HMJLFLJH_00002 [Genus species]" , molinfo { biomol peptide , tech concept-trans } } , @@ -239,7 +239,7 @@ { data gene { - locus-tag "PROKKA_00001" } } } } , + locus-tag "HMJLFLJH_00001" } } } } , { id local @@ -269,7 +269,7 @@ { data gene { - locus-tag "PROKKA_00002" } } } } } } } } , + locus-tag "HMJLFLJH_00002" } } } } } } } } , seq { id { local @@ -286,7 +286,7 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -311,17 +311,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , inst { repr raw , mol dna , @@ -342,7 +342,7 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -367,17 +367,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , seq-set { seq { id { @@ -413,7 +413,7 @@ local str "contig4_1" } , descr { - title "hypothetical protein PROKKA_00003 [Genus species]" , + title "hypothetical protein HMJLFLJH_00003 [Genus species]" , molinfo { biomol peptide , tech concept-trans } } , @@ -478,7 +478,7 @@ { data gene { - locus-tag "PROKKA_00003" } } } } } } } } , + locus-tag "HMJLFLJH_00003" } } } } } } } } , set { class nuc-prot , descr { @@ -491,7 +491,7 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -516,17 +516,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , seq-set { seq { id { @@ -552,7 +552,7 @@ local str "contig5_1" } , descr { - title "hypothetical protein PROKKA_00004 [Genus species]" , + title "hypothetical protein HMJLFLJH_00004 [Genus species]" , molinfo { biomol peptide , tech concept-trans } } , @@ -614,7 +614,7 @@ { data gene { - locus-tag "PROKKA_00004" } } } } } } } } , + locus-tag "HMJLFLJH_00004" } } } } } } } } , set { class nuc-prot , descr { @@ -627,7 +627,7 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -652,17 +652,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , seq-set { seq { id { @@ -707,7 +707,7 @@ local str "contig6_1" } , descr { - title "hypothetical protein PROKKA_00005 [Genus species]" , + title "hypothetical protein HMJLFLJH_00005 [Genus species]" , molinfo { biomol peptide , tech concept-trans } } , @@ -772,7 +772,7 @@ { data gene { - locus-tag "PROKKA_00005" } } } } } } } } , + locus-tag "HMJLFLJH_00005" } } } } } } } } , seq { id { local @@ -789,7 +789,7 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.12 from + comment "Annotated using prokka 1.13 from https://github.com/tseemann/prokka" , user { type @@ -814,17 +814,17 @@ label str "day" , data - int 21 } , + int 27 } , { label str "year" , data - int 2017 } } } , + int 2018 } } } , create-date std { - year 2017 , + year 2018 , month 3 , - day 21 } } , + day 27 } } , inst { repr raw , mol dna , diff -r a17498c603ec -r eaee459f3d69 test-data/out.tbl --- a/test-data/out.tbl Tue Mar 21 10:13:06 2017 -0400 +++ b/test-data/out.tbl Wed Mar 28 12:38:42 2018 -0400 @@ -2,26 +2,26 @@ >Feature contig2 40 498 CDS inference ab initio prediction:Prodigal:2.6 - locus_tag PROKKA_00001 + locus_tag HMJLFLJH_00001 product hypothetical protein 498 614 CDS inference ab initio prediction:Prodigal:2.6 - locus_tag PROKKA_00002 + locus_tag HMJLFLJH_00002 product hypothetical protein >Feature contig3 >Feature contig4 21 884 CDS inference ab initio prediction:Prodigal:2.6 - locus_tag PROKKA_00003 + locus_tag HMJLFLJH_00003 product hypothetical protein >Feature contig5 275 406 CDS inference ab initio prediction:Prodigal:2.6 - locus_tag PROKKA_00004 + locus_tag HMJLFLJH_00004 product hypothetical protein >Feature contig6 6 767 CDS inference ab initio prediction:Prodigal:2.6 - locus_tag PROKKA_00005 + locus_tag HMJLFLJH_00005 product hypothetical protein >Feature contig7 diff -r a17498c603ec -r eaee459f3d69 test-data/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.tsv Wed Mar 28 12:38:42 2018 -0400 @@ -0,0 +1,6 @@ +locus_tag ftype length_bp gene EC_number COG product +HMJLFLJH_00001 CDS 459 hypothetical protein +HMJLFLJH_00002 CDS 117 hypothetical protein +HMJLFLJH_00003 CDS 864 hypothetical protein +HMJLFLJH_00004 CDS 132 hypothetical protein +HMJLFLJH_00005 CDS 762 hypothetical protein