changeset 13:a17498c603ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
author iuc
date Tue, 21 Mar 2017 10:13:06 -0400
parents da479161bbe4
children eaee459f3d69
files prokka.xml readme.rst test-data/out.err test-data/out.gbk test-data/out.gff test-data/out.sqn test-data/out.tbl
diffstat 7 files changed, 247 insertions(+), 141 deletions(-) [+]
line wrap: on
line diff
--- a/prokka.xml	Fri Jan 20 03:39:08 2017 -0500
+++ b/prokka.xml	Tue Mar 21 10:13:06 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="prokka" name="Prokka" version="1.11.1">
+<tool id="prokka" name="Prokka" version="1.12.0">
     <description>prokaryotic genome annotation</description>
     <requirements>
-        <requirement type="package" version="1.11">prokka</requirement>
+        <requirement type="package" version="1.12">prokka</requirement>
     </requirements>
     <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
     <stdio>
@@ -189,7 +189,7 @@
             <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.err" file="out.err" />
+            <output name="out_err" file="out.err" />
             <output name="out_txt" file="out.txt" />
             <output name="out_log">
                 <assert_contents>
@@ -203,7 +203,7 @@
 
 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
 
-.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
+.. _Prokka: http://github.com/tseemann/prokka
 
 **Output files**
 
@@ -219,7 +219,7 @@
 
 You can use this tool only if you agree to the license terms of: `Prokka`_.
 
-.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
+.. _Prokka: http://github.com/tseemann/prokka
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu135</citation>
--- a/readme.rst	Fri Jan 20 03:39:08 2017 -0500
+++ b/readme.rst	Tue Mar 21 10:13:06 2017 -0400
@@ -9,6 +9,7 @@
 Version history
 ---------------
 
+- Release 9 (prokka 1.12.0): Support Prokka 1.12. Uses updated conda dependency 1.12
 - Release 8 (prokka 1.11.1): Use Conda for installing tool dependencies, ToolShed dependencies are not supported anymore. Add a test. The tool is now maintained by the IUC.
 - Release 7 (prokka 1.11.0): Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.
 - Release 6 (prokka 1.4.0): Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
--- a/test-data/out.err	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.err	Tue Mar 21 10:13:06 2017 -0400
@@ -1,46 +1,144 @@
->PROKKA_00001 hypothetical protein
-ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC
-ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC
-AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT
-GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC
-GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC
-GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG
-TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
-AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
->PROKKA_00002 hypothetical protein
-ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT
-ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
->PROKKA_00003 hypothetical protein
-ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT
-TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT
-GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT
-TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC
-TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG
-TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
-CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT
-CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG
-TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT
-CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG
-CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
-CGCGATTCAATCATGACTTCGTGA
->PROKKA_00004 hypothetical protein
-TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT
-TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA
-ACAATACTGTAG
->PROKKA_00005 hypothetical protein
-ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT
-TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG
-GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT
-GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT
-AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
-ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA
-AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA
-AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA
-GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT
-AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT
-ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT
-GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC
-GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
+Discrepancy Report Results
+
+Summary
+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
+FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
+DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
+DISC_FEATURE_COUNT:CDS: 5 present
+DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
+FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
+NO_ANNOTATION:3 bioseqs have no features
+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
+ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
+SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
+MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
+MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
+TECHNIQUE_NOT_TSA:7 technique are not set as TSA
+MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
+MISSING_PROJECT:12 sequences do not include project.
+DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
+
+
+Detailed Report
+
+DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
+
+FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6_1 (length 253)
+
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
+DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+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
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig2:498-614	PROKKA_00002
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig4:21-884	PROKKA_00003
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig5:275-406	PROKKA_00004
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig6:6-767	PROKKA_00005
+
+DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig7 (length 276)
+
+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
+
+DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig5_1 (length 43)
+
+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig6_1 (length 253)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
--- a/test-data/out.gbk	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.gbk	Tue Mar 21 10:13:06 2017 -0400
@@ -1,4 +1,4 @@
-LOCUS       contig1                  350 bp    DNA     linear       11-OCT-2016
+LOCUS       contig1                  350 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -6,7 +6,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..350
                      /organism="Genus species"
@@ -20,7 +21,7 @@
       241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
       301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc
 //
-LOCUS       contig2                  840 bp    DNA     linear       11-OCT-2016
+LOCUS       contig2                  840 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -28,7 +29,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..840
                      /organism="Genus species"
@@ -36,7 +38,7 @@
                      /strain="strain"
      CDS             40..498
                      /locus_tag="PROKKA_00001"
-                     /inference="ab initio prediction:Prodigal:2.60"
+                     /inference="ab initio prediction:Prodigal:2.6"
                      /codon_start=1
                      /transl_table=11
                      /product="hypothetical protein"
@@ -45,7 +47,7 @@
                      FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"
      CDS             498..614
                      /locus_tag="PROKKA_00002"
-                     /inference="ab initio prediction:Prodigal:2.60"
+                     /inference="ab initio prediction:Prodigal:2.6"
                      /codon_start=1
                      /transl_table=11
                      /product="hypothetical protein"
@@ -66,7 +68,7 @@
       721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga
       781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta
 //
-LOCUS       contig3                  210 bp    DNA     linear       11-OCT-2016
+LOCUS       contig3                  210 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -74,7 +76,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..210
                      /organism="Genus species"
@@ -86,7 +89,7 @@
       121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt
       181 tgtttcaggg ttatttgaat atctataaca
 //
-LOCUS       contig4                 1260 bp    DNA     linear       11-OCT-2016
+LOCUS       contig4                 1260 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -94,7 +97,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..1260
                      /organism="Genus species"
@@ -102,7 +106,7 @@
                      /strain="strain"
      CDS             21..884
                      /locus_tag="PROKKA_00003"
-                     /inference="ab initio prediction:Prodigal:2.60"
+                     /inference="ab initio prediction:Prodigal:2.6"
                      /codon_start=1
                      /transl_table=11
                      /product="hypothetical protein"
@@ -135,7 +139,7 @@
      1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc
      1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc
 //
-LOCUS       contig5                  490 bp    DNA     linear       11-OCT-2016
+LOCUS       contig5                  490 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -143,7 +147,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..490
                      /organism="Genus species"
@@ -151,7 +156,7 @@
                      /strain="strain"
      CDS             275..406
                      /locus_tag="PROKKA_00004"
-                     /inference="ab initio prediction:Prodigal:2.60"
+                     /inference="ab initio prediction:Prodigal:2.6"
                      /codon_start=1
                      /transl_table=11
                      /product="hypothetical protein"
@@ -167,7 +172,7 @@
       421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt
       481 tttgtttctg
 //
-LOCUS       contig6                 1960 bp    DNA     linear       11-OCT-2016
+LOCUS       contig6                 1960 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -175,7 +180,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..1960
                      /organism="Genus species"
@@ -183,7 +189,7 @@
                      /strain="strain"
      CDS             6..767
                      /locus_tag="PROKKA_00005"
-                     /inference="ab initio prediction:Prodigal:2.60"
+                     /inference="ab initio prediction:Prodigal:2.6"
                      /codon_start=1
                      /transl_table=11
                      /product="hypothetical protein"
@@ -227,7 +233,7 @@
      1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta
      1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact
 //
-LOCUS       contig7                  276 bp    DNA     linear       11-OCT-2016
+LOCUS       contig7                  276 bp    DNA     linear       21-MAR-2017
 DEFINITION  Genus species strain strain.
 ACCESSION   
 VERSION
@@ -235,7 +241,8 @@
 SOURCE      Genus species
   ORGANISM  Genus species
             Unclassified.
-COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+COMMENT     Annotated using prokka 1.12 from
+            https://github.com/tseemann/prokka.
 FEATURES             Location/Qualifiers
      source          1..276
                      /organism="Genus species"
--- a/test-data/out.gff	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.gff	Tue Mar 21 10:13:06 2017 -0400
@@ -6,11 +6,11 @@
 ##sequence-region contig5 1 490
 ##sequence-region contig6 1 1960
 ##sequence-region contig7 1 276
-contig2	Prodigal:2.60	CDS	40	498	.	+	0	ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00001;product=hypothetical protein
-contig2	Prodigal:2.60	CDS	498	614	.	+	0	ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00002;product=hypothetical protein
-contig4	Prodigal:2.60	CDS	21	884	.	+	0	ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00003;product=hypothetical protein
-contig5	Prodigal:2.60	CDS	275	406	.	+	0	ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00004;product=hypothetical protein
-contig6	Prodigal:2.60	CDS	6	767	.	+	0	ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00005;product=hypothetical protein
+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
 ##FASTA
 >contig1
 GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
--- a/test-data/out.sqn	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.sqn	Tue Mar 21 10:13:06 2017 -0400
@@ -17,8 +17,8 @@
               gcode 11 } } } ,
         molinfo {
           biomol genomic } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -37,22 +37,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       inst {
         repr raw ,
         mol dna ,
@@ -75,8 +75,8 @@
                   subtype strain ,
                   subname "strain" } } ,
               gcode 11 } } } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -95,22 +95,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       seq-set {
         seq {
           id {
@@ -234,7 +234,7 @@
                 qual {
                   {
                     qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.60" } } ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
                 xref {
                   {
                     data
@@ -264,7 +264,7 @@
                 qual {
                   {
                     qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.60" } } ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
                 xref {
                   {
                     data
@@ -286,8 +286,8 @@
               gcode 11 } } } ,
         molinfo {
           biomol genomic } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -306,22 +306,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       inst {
         repr raw ,
         mol dna ,
@@ -342,8 +342,8 @@
                   subtype strain ,
                   subname "strain" } } ,
               gcode 11 } } } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -362,22 +362,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       seq-set {
         seq {
           id {
@@ -473,7 +473,7 @@
                 qual {
                   {
                     qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.60" } } ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
                 xref {
                   {
                     data
@@ -491,8 +491,8 @@
                   subtype strain ,
                   subname "strain" } } ,
               gcode 11 } } } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -511,22 +511,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       seq-set {
         seq {
           id {
@@ -609,7 +609,7 @@
                 qual {
                   {
                     qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.60" } } ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
                 xref {
                   {
                     data
@@ -627,8 +627,8 @@
                   subtype strain ,
                   subname "strain" } } ,
               gcode 11 } } } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -647,22 +647,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       seq-set {
         seq {
           id {
@@ -767,7 +767,7 @@
                 qual {
                   {
                     qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.60" } } ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
                 xref {
                   {
                     data
@@ -789,8 +789,8 @@
               gcode 11 } } } ,
         molinfo {
           biomol genomic } ,
-        comment "Annotated using prokka 1.11 from
- http://www.vicbioinformatics.com" ,
+        comment "Annotated using prokka 1.12 from
+ https://github.com/tseemann/prokka" ,
         user {
           type
             str "NcbiCleanup" ,
@@ -809,22 +809,22 @@
               label
                 str "month" ,
               data
-                int 10 } ,
+                int 3 } ,
             {
               label
                 str "day" ,
               data
-                int 11 } ,
+                int 21 } ,
             {
               label
                 str "year" ,
               data
-                int 2016 } } } ,
+                int 2017 } } } ,
         create-date
           std {
-            year 2016 ,
-            month 10 ,
-            day 11 } } ,
+            year 2017 ,
+            month 3 ,
+            day 21 } } ,
       inst {
         repr raw ,
         mol dna ,
--- a/test-data/out.tbl	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.tbl	Tue Mar 21 10:13:06 2017 -0400
@@ -1,27 +1,27 @@
 >Feature contig1
 >Feature contig2
 40	498	CDS
-			inference	ab initio prediction:Prodigal:2.60
+			inference	ab initio prediction:Prodigal:2.6
 			locus_tag	PROKKA_00001
 			product	hypothetical protein
 498	614	CDS
-			inference	ab initio prediction:Prodigal:2.60
+			inference	ab initio prediction:Prodigal:2.6
 			locus_tag	PROKKA_00002
 			product	hypothetical protein
 >Feature contig3
 >Feature contig4
 21	884	CDS
-			inference	ab initio prediction:Prodigal:2.60
+			inference	ab initio prediction:Prodigal:2.6
 			locus_tag	PROKKA_00003
 			product	hypothetical protein
 >Feature contig5
 275	406	CDS
-			inference	ab initio prediction:Prodigal:2.60
+			inference	ab initio prediction:Prodigal:2.6
 			locus_tag	PROKKA_00004
 			product	hypothetical protein
 >Feature contig6
 6	767	CDS
-			inference	ab initio prediction:Prodigal:2.60
+			inference	ab initio prediction:Prodigal:2.6
 			locus_tag	PROKKA_00005
 			product	hypothetical protein
 >Feature contig7