# HG changeset patch
# User pimarin
# Date 1673522717 0
# Node ID 44fb905481f097faf39199211f67ac2a1fadf39c
# Parent  591cae6ef29dd5f79ca441171712e42d911856f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit a7dcdae8bccb5a8d7abdb9c6d058f9bd7c6f6c15

diff -r 591cae6ef29d -r 44fb905481f0 bakta.xml
--- a/bakta.xml	Thu Dec 22 15:06:32 2022 +0000
+++ b/bakta.xml	Thu Jan 12 11:25:17 2023 +0000
@@ -12,8 +12,8 @@
 
     <command detect_errors="aggressive"><![CDATA[
         mkdir ./database_path &&
-        ln -s '$(input_option.bakta_db_select.fields.path)/'* database_path &&
-        ln -s '$(input_option.amrfinder_db_select.fields.path)' database_path &&
+        ln -s '$(input_option.bakta_db_select.fields.path)/*' database_path &&
+        ln -rs '$(input_option.amrfinder_db_select.fields.path)' database_path/latest &&
 
         bakta
         #*======================================
@@ -92,10 +92,6 @@
             <param name="bakta_db_select" type="select" label="The bakta database">
                 <options from_data_table="bakta_database">
                   <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/>
-                  <column name="value" index="0"/>
-                  <column name="dbkey" index="1"/>
-                  <column name="bakta_version" index="2"/>
-                  <column name="path" index="3"/>
                   <validator message="No bakta database is available" type="no_options"/>
                 </options>
             </param>
diff -r 591cae6ef29d -r 44fb905481f0 macro.xml
--- a/macro.xml	Thu Dec 22 15:06:32 2022 +0000
+++ b/macro.xml	Thu Jan 12 11:25:17 2023 +0000
@@ -2,6 +2,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.6.1</token>
     <token name="@BAKTA_VERSION@">1.5</token>
+    <token name="@DEEPSIG@">1.2.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
@@ -20,6 +21,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bakta</requirement>
+            <requirement type="package" version="@DEEPSIG@">deepsig </requirement>            
         </requirements>
     </xml>
     <xml name="citations">
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.embl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.embl	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,88 @@
+ID   contig_1; ; circular; DNA; ; PRO; 1330 BP.
+XX
+AC   contig_1;
+XX
+DE   plasmid unnamed1, complete sequence
+XX
+OS   .
+OC   .
+XX
+CC   Annotated with Bakta
+CC   Software: v1.6.1
+CC   Database: v4.0
+CC   DOI: 10.1099/mgen.0.000685
+CC   URL: github.com/oschwengers/bakta
+CC   
+CC   ##Genome Annotation Summary:##
+CC   Annotation Date                :: 01/03/2023, 10:02:08
+CC   Annotation Pipeline            :: Bakta
+CC   Annotation Software version    ::  v1.6.1
+CC   Annotation Database version    ::  v4.0
+CC   CDSs                           ::     2
+CC   tRNAs                          ::     0
+CC   tmRNAs                         ::     0
+CC   rRNAs                          ::     0
+CC   ncRNAs                         ::     0
+CC   regulatory ncRNAs              ::     0
+CC   CRISPR Arrays                  ::     0
+CC   oriCs/oriVs                    ::     0
+CC   oriTs                          ::     0
+CC   gaps                           ::     0
+CC   pseudogenes                    ::     0
+XX
+FH   Key             Location/Qualifiers
+FH
+FT   source          1..1330
+FT                   /mol_type="genomic DNA"
+FT                   /plasmid="unnamed1"
+FT   gene            413..736
+FT                   /locus_tag="IHHALP_00005"
+FT   CDS             413..736
+FT                   /product="hypothetical protein"
+FT                   /locus_tag="IHHALP_00005"
+FT                   /protein_id="gnl|Bakta|IHHALP_00005"
+FT                   /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
+FT                   AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
+FT                   MAD"
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /inference="ab initio prediction:Prodigal:2.6"
+FT   gene            complement(join(971..1330,1..141))
+FT                   /locus_tag="IHHALP_00010"
+FT   CDS             complement(join(971..1330,1..141))
+FT                   /product="hypothetical protein"
+FT                   /locus_tag="IHHALP_00010"
+FT                   /protein_id="gnl|Bakta|IHHALP_00010"
+FT                   /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
+FT                   EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
+FT                   YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
+FT                   IPI"
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /inference="ab initio prediction:Prodigal:2.6"
+XX
+SQ   Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other;
+     ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc        60
+     gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc       120
+     agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg       180
+     tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt       240
+     tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt       300
+     gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac       360
+     cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa       420
+     acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga       480
+     agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt       540
+     acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga       600
+     agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga       660
+     cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag       720
+     gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt       780
+     aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga       840
+     tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc       900
+     agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc       960
+     tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa      1020
+     ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat      1080
+     cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat      1140
+     taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa      1200
+     aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc      1260
+     tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg      1320
+     cttctatttg                                                             1330
+//
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.faa	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD
+>IHHALP_00010 hypothetical protein
+MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.ffn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.ffn	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG
+>IHHALP_00010 hypothetical protein
+ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.fna	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,24 @@
+>contig_1 [completeness=complete] [topology=circular] [gcode=11]
+TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC
+GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC
+AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG
+TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT
+TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT
+GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC
+CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA
+ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA
+AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT
+ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA
+AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA
+CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG
+GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT
+AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA
+TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC
+AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC
+TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA
+GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT
+CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT
+TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA
+AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC
+TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG
+CTTCTATTTG
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.gbff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.gbff	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,84 @@
+LOCUS       contig_1                1330 bp    DNA     circular BCT 03-JAN-2023
+DEFINITION  plasmid unnamed1, complete sequence.
+ACCESSION   contig_1
+VERSION     contig_1
+KEYWORDS    .
+SOURCE      None
+  ORGANISM  .
+            .
+COMMENT     Annotated with Bakta
+            Software: v1.6.1
+            Database: v4.0
+            DOI: 10.1099/mgen.0.000685
+            URL: github.com/oschwengers/bakta
+            
+            ##Genome Annotation Summary:##
+            Annotation Date                :: 01/03/2023, 10:02:08
+            Annotation Pipeline            :: Bakta
+            Annotation Software version    ::  v1.6.1
+            Annotation Database version    ::  v4.0
+            CDSs                           ::     2
+            tRNAs                          ::     0
+            tmRNAs                         ::     0
+            rRNAs                          ::     0
+            ncRNAs                         ::     0
+            regulatory ncRNAs              ::     0
+            CRISPR Arrays                  ::     0
+            oriCs/oriVs                    ::     0
+            oriTs                          ::     0
+            gaps                           ::     0
+            pseudogenes                    ::     0
+FEATURES             Location/Qualifiers
+     source          1..1330
+                     /mol_type="genomic DNA"
+                     /plasmid="unnamed1"
+     gene            413..736
+                     /locus_tag="IHHALP_00005"
+     CDS             413..736
+                     /product="hypothetical protein"
+                     /locus_tag="IHHALP_00005"
+                     /protein_id="gnl|Bakta|IHHALP_00005"
+                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
+                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
+                     MAD"
+                     /codon_start=1
+                     /transl_table=11
+                     /inference="ab initio prediction:Prodigal:2.6"
+     gene            complement(join(971..1330,1..141))
+                     /locus_tag="IHHALP_00010"
+     CDS             complement(join(971..1330,1..141))
+                     /product="hypothetical protein"
+                     /locus_tag="IHHALP_00010"
+                     /protein_id="gnl|Bakta|IHHALP_00010"
+                     /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
+                     EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
+                     YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
+                     IPI"
+                     /codon_start=1
+                     /transl_table=11
+                     /inference="ab initio prediction:Prodigal:2.6"
+ORIGIN
+        1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc
+       61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc
+      121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg
+      181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt
+      241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt
+      301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac
+      361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa
+      421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga
+      481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt
+      541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga
+      601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga
+      661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag
+      721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt
+      781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga
+      841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc
+      901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc
+      961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa
+     1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat
+     1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat
+     1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa
+     1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc
+     1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg
+     1321 cttctatttg
+//
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.gff3	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,36 @@
+##gff-version 3
+##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
+# Annotated with Bakta
+# Software: v1.6.1
+# Database: v4.0
+# DOI: 10.1099/mgen.0.000685
+# URL: github.com/oschwengers/bakta
+##sequence-region contig_1 1 1330
+contig_1	Bakta	region	1	1330	.	+	.	ID=contig_1;Name=contig_1;Is_circular=true
+contig_1	Prodigal	CDS	413	736	.	+	0	ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein
+contig_1	Prodigal	CDS	971	1471	.	-	0	ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein
+##FASTA
+>contig_1
+TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC
+GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC
+AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG
+TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT
+TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT
+GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC
+CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA
+ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA
+AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT
+ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA
+AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA
+CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG
+GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT
+AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA
+TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC
+AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC
+TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA
+GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT
+CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT
+TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA
+AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC
+TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG
+CTTCTATTTG
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.hypotheticals.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.hypotheticals.faa	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD
+>IHHALP_00010 hypothetical protein
+MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.hypotheticals.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,5 @@
+#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta
+#Database v4.0, https://doi.org/10.5281/zenodo.4247252
+#Sequence Id	Start	Stop	Strand	Locus Tag	Mol Weight [kDa]	Iso El. Point	Pfam hits	Dbxrefs
+contig_1	413	736	+	IHHALP_00005	12.1	10.4		
+contig_1	971	141	-	IHHALP_00010	18.9	7.7		
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.json	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,90 @@
+{
+    "genome": {
+        "genus": null,
+        "species": null,
+        "strain": null,
+        "complete": true,
+        "gram": "?",
+        "translation_table": 11
+    },
+    "stats": {
+        "no_sequences": 1,
+        "size": 1330,
+        "gc": 0.4518796992481203,
+        "n_ratio": 0.0,
+        "n50": 1330,
+        "coding_ratio": 0.6203007518796992
+    },
+    "features": [
+        {
+            "type": "cds",
+            "contig": "contig_1",
+            "start": 413,
+            "stop": 736,
+            "strand": "+",
+            "gene": null,
+            "product": "hypothetical protein",
+            "start_type": "ATG",
+            "rbs_motif": "GGAG/GAGG",
+            "db_xrefs": [],
+            "frame": 2,
+            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
+            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
+            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
+            "hypothetical": true,
+            "seq_stats": {
+                "molecular_weight": 12072.90819999999,
+                "isoelectric_point": 10.367886161804197
+            },
+            "id": "IHHALPPJCH_1",
+            "locus": "IHHALP_00005"
+        },
+        {
+            "type": "cds",
+            "contig": "contig_1",
+            "start": 971,
+            "stop": 141,
+            "strand": "-",
+            "gene": null,
+            "product": "hypothetical protein",
+            "start_type": "ATG",
+            "rbs_motif": "AGGA/GGAG/GAGG",
+            "db_xrefs": [],
+            "frame": 1,
+            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
+            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
+            "edge": true,
+            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
+            "hypothetical": true,
+            "seq_stats": {
+                "molecular_weight": 18866.325799999995,
+                "isoelectric_point": 7.696590614318848
+            },
+            "id": "IHHALPPJCH_2",
+            "locus": "IHHALP_00010"
+        }
+    ],
+    "sequences": [
+        {
+            "id": "contig_1",
+            "description": "[completeness=complete] [topology=circular] [gcode=11]",
+            "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG",
+            "length": 1330,
+            "complete": true,
+            "type": "plasmid",
+            "topology": "circular",
+            "simple_id": "contig_1",
+            "orig_id": "NC_002127.1",
+            "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence",
+            "name": "unnamed1"
+        }
+    ],
+    "run": {
+        "start": "2023-01-03 10:02:07",
+        "end": "2023-01-03 10:02:08"
+    },
+    "version": {
+        "bakta": "1.6.1",
+        "db": "4.0"
+    }
+}
\ No newline at end of file
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.log
--- a/test-data/TEST_1/TEST_1.log	Thu Dec 22 15:06:32 2022 +0000
+++ b/test-data/TEST_1/TEST_1.log	Thu Jan 12 11:25:17 2023 +0000
@@ -79,11 +79,7 @@
 	oriCs/oriVs: 0
 	oriTs: 0
 
-<<<<<<< HEAD
-export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/2/working
-=======
-export annotation results to: /tmp/tmp4jorszj6/job_working_directory/000/2/working
->>>>>>> 195c8410c (change option for plot)
+export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/2/working
 	human readable TSV...
 	GFF3...
 	INSDC GenBank & EMBL...
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.tsv	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,5 @@
+#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta
+#Database (v4.0): https://doi.org/10.5281/zenodo.4247252
+#Sequence Id	Type	Start	Stop	Strand	Locus Tag	Gene	Product	DbXrefs
+contig_1	cds	413	736	+	IHHALP_00005		hypothetical protein	
+contig_1	cds	971	141	-	IHHALP_00010		hypothetical protein	
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_1/TEST_1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_1/TEST_1.txt	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,30 @@
+Sequence(s):
+Length: 1330
+Count: 1
+GC: 45.2
+N50: 1330
+N ratio: 0.0
+coding density: 62.0
+
+Annotation:
+tRNAs: 0
+tmRNAs: 0
+rRNAs: 0
+ncRNAs: 0
+ncRNA regions: 0
+CRISPR arrays: 0
+CDSs: 2
+pseudogenes: 0
+hypotheticals: 2
+signal peptides: 0
+sORFs: 0
+gaps: 0
+oriCs: 0
+oriVs: 0
+oriTs: 0
+
+Bakta:
+Software: v1.6.1
+Database: v4.0
+DOI: 10.1099/mgen.0.000685
+URL: github.com/oschwengers/bakta
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_2/TEST_2.ffn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_2/TEST_2.ffn	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG
+>IHHALP_00010 hypothetical protein
+ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_3/TEST_3.ffn
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_4/TEST_4.ffn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_4/TEST_4.ffn	Thu Jan 12 11:25:17 2023 +0000
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG
+>IHHALP_00010 hypothetical protein
+ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
diff -r 591cae6ef29d -r 44fb905481f0 test-data/TEST_5/TEST_5.log
--- a/test-data/TEST_5/TEST_5.log	Thu Dec 22 15:06:32 2022 +0000
+++ b/test-data/TEST_5/TEST_5.log	Thu Jan 12 11:25:17 2023 +0000
@@ -43,11 +43,7 @@
 	oriCs/oriVs: 0
 	oriTs: 0
 
-<<<<<<< HEAD
-export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/14/working
-=======
-export annotation results to: /tmp/tmp4jorszj6/job_working_directory/000/14/working
->>>>>>> 195c8410c (change option for plot)
+export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working
 	human readable TSV...
 	GFF3...
 	INSDC GenBank & EMBL...