Mercurial > repos > crs4 > prokka
changeset 14:eaee459f3d69 draft
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 | 3a0bd09a41dd |
| files | prokka.xml test-data/out.err test-data/out.faa test-data/out.ffn test-data/out.gbk test-data/out.gff test-data/out.sqn test-data/out.tbl test-data/out.tsv |
| diffstat | 9 files changed, 115 insertions(+), 107 deletions(-) [+] |
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--- 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 @@ -<tool id="prokka" name="Prokka" version="1.12.0"> - <description>prokaryotic genome annotation</description> +<tool id="prokka" name="Prokka" version="1.13"> + <description>Prokaryotic genome annotation</description> <requirements> - <requirement type="package" version="1.12">prokka</requirement> + <requirement type="package" version="1.13">prokka</requirement> </requirements> - <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> - <stdio> - <exit_code range="1:" /> - </stdio> + <version_command>prokka --version</version_command> - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ prokka --cpus \${GALAXY_SLOTS:-8} --quiet ## to avoid non-error messages written to stderr @@ -77,7 +74,7 @@ ]]></command> <inputs> <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> - <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" /> + <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" /> <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" /> <param name="gffver" type="select" label="GFF version (--gffver)"> <option value="3">3</option> @@ -139,6 +136,7 @@ <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option> <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option> <option value="tbl" selected="True">Feature Table file (.tbl)</option> + <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option> <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option> <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> </param> @@ -169,6 +167,9 @@ <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> <filter>outputs and 'tbl' in outputs</filter> </data> + <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv"> + <filter>outputs and 'tsv' in outputs</filter> + </data> <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> <filter>outputs and 'err' in outputs</filter> </data> @@ -180,7 +181,7 @@ <tests> <test> <param name="input" ftype="fasta" value="phiX174.fasta" /> - <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" /> + <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" /> <output name="out_gff" file="out.gff" /> <output name="out_gbk" file="out.gbk" lines_diff="14" /> <output name="out_fna" file="out.fna" /> @@ -189,6 +190,7 @@ <output name="out_sqn" file="out.sqn" lines_diff="84" /> <output name="out_fsa" file="out.fsa" /> <output name="out_tbl" file="out.tbl" /> + <output name="out_tsv" file="out.tsv" /> <output name="out_err" file="out.err" /> <output name="out_txt" file="out.txt" /> <output name="out_log"> @@ -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/
--- 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)
--- 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
--- 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
--- 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
--- 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
--- 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 ,
--- 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
--- /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