# HG changeset patch
# User pimarin
# Date 1676288226 0
# Node ID f93f54a21132ca1534e611a00107a4c50028518a
# Parent  ed4bc0577be65d1f5c515fbee53105d0502a5bba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit ed22b0f3b7b651e240154a08c9313585def1cfe5

diff -r ed4bc0577be6 -r f93f54a21132 bakta.xml
--- a/bakta.xml	Mon Jan 23 16:41:16 2023 +0000
+++ b/bakta.xml	Mon Feb 13 11:37:06 2023 +0000
@@ -88,7 +88,7 @@
         <section name="input_option" title="Input/Output options" expanded="true">
             <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"/>
+                  <filter type="static_value" value="@BAKTA_VERSION@" column="2"/>
                   <validator message="No bakta database is available" type="no_options"/>
                 </options>
             </param>
@@ -125,7 +125,7 @@
                 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
             </param>
             <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
-            <param argument="--replicons" type="data" format="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
+            <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
             <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
             <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
         </section>
@@ -210,7 +210,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="250"/>
            </section>
            <section name="output_files">
@@ -238,7 +238,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="250"/>
            </section>
            <section name="organism">
@@ -274,7 +274,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="350"/>
            </section>
            <section name="workflow">
@@ -293,15 +293,15 @@
              <section name="input_option" >
                  <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                  <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna"/>
+                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
              </section>
              <section name="annotation">
                  <param name="complete" value="true"/>
                  <param name="prodigal" value="prodigal.tf"/>
                  <param name="translation_table" value="4"/>
-                 <param name="replicons" value="replicons.tsv"/>
+                 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
                  <param name="compliant" value="true"/>
-                 <param name="proteins" value="user-proteins.faa"/>
+                 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
              </section>
              <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
              <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
@@ -316,7 +316,7 @@
              <section name="input_option" >
                  <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                  <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna"/>
+                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
              </section>
              <section name="annotation">
                  <param name="complete" value="true"/>
diff -r ed4bc0577be6 -r f93f54a21132 test-data/TEST_1/TEST_1.embl
--- a/test-data/TEST_1/TEST_1.embl	Mon Jan 23 16:41:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.embl	Mon Feb 13 11:37:06 2023 +0000
@@ -14,7 +14,7 @@
 CC   URL: github.com/oschwengers/bakta
 CC   
 CC   ##Genome Annotation Summary:##
-CC   Annotation Date                :: 01/03/2023, 10:02:08
+CC   Annotation Date                :: 02/10/2023, 11:57:30
 CC   Annotation Pipeline            :: Bakta
 CC   Annotation Software version    ::  v1.6.1
 CC   Annotation Database version    ::  v4.0
diff -r ed4bc0577be6 -r f93f54a21132 test-data/TEST_1/TEST_1.gbff
--- a/test-data/TEST_1/TEST_1.gbff	Mon Jan 23 16:41:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.gbff	Mon Feb 13 11:37:06 2023 +0000
@@ -1,4 +1,4 @@
-LOCUS       contig_1                1330 bp    DNA     circular BCT 03-JAN-2023
+LOCUS       contig_1                1330 bp    DNA     circular BCT 10-FEB-2023
 DEFINITION  plasmid unnamed1, complete sequence.
 ACCESSION   contig_1
 VERSION     contig_1
@@ -13,7 +13,7 @@
             URL: github.com/oschwengers/bakta
             
             ##Genome Annotation Summary:##
-            Annotation Date                :: 01/03/2023, 10:02:08
+            Annotation Date                :: 02/10/2023, 11:57:30
             Annotation Pipeline            :: Bakta
             Annotation Software version    ::  v1.6.1
             Annotation Database version    ::  v4.0
diff -r ed4bc0577be6 -r f93f54a21132 test-data/TEST_1/TEST_1.json
--- a/test-data/TEST_1/TEST_1.json	Mon Jan 23 16:41:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.json	Mon Feb 13 11:37:06 2023 +0000
@@ -80,8 +80,8 @@
         }
     ],
     "run": {
-        "start": "2023-01-03 10:02:07",
-        "end": "2023-01-03 10:02:08"
+        "start": "2023-02-10 11:57:29",
+        "end": "2023-02-10 11:57:30"
     },
     "version": {
         "bakta": "1.6.1",
diff -r ed4bc0577be6 -r f93f54a21132 test-data/TEST_1/TEST_1.log
--- a/test-data/TEST_1/TEST_1.log	Mon Jan 23 16:41:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.log	Mon Feb 13 11:37:06 2023 +0000
@@ -79,7 +79,7 @@
 	oriCs/oriVs: 0
 	oriTs: 0
 
-export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/2/working
+export annotation results to: /tmp/tmp3ft3p63j/job_working_directory/000/2/working
 	human readable TSV...
 	GFF3...
 	INSDC GenBank & EMBL...
diff -r ed4bc0577be6 -r f93f54a21132 test-data/TEST_5/TEST_5.log
--- a/test-data/TEST_5/TEST_5.log	Mon Jan 23 16:41:16 2023 +0000
+++ b/test-data/TEST_5/TEST_5.log	Mon Feb 13 11:37:06 2023 +0000
@@ -43,7 +43,7 @@
 	oriCs/oriVs: 0
 	oriTs: 0
 
-export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working
+export annotation results to: /tmp/tmp3ft3p63j/job_working_directory/000/14/working
 	human readable TSV...
 	GFF3...
 	INSDC GenBank & EMBL...
diff -r ed4bc0577be6 -r f93f54a21132 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Jan 23 16:41:16 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 13 11:37:06 2023 +0000
@@ -2,6 +2,10 @@
 <tables>
     <table name="bakta_database" comment_char="#">
         <columns>value, dbkey, bakta_version, path</columns>
-        <file path="tool-data/bakta_database.loc.sample" />
+        <file path="tool-data/bakta_database.loc.sample"/>
+    </table>
+    <table name="amrfinderplus_database" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/amrfinderplus_database.loc.sample"/>
     </table>
 </tables>
diff -r ed4bc0577be6 -r f93f54a21132 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Mon Jan 23 16:41:16 2023 +0000
+++ b/tool_data_table_conf.xml.test	Mon Feb 13 11:37:06 2023 +0000
@@ -7,6 +7,5 @@
     <table name="amrfinderplus_database" comment_char="#">
         <columns>value, name, path</columns>
         <file path="${__HERE__}/test-data/amrfinderplus_database.loc" />
-
     </table>
 </tables>