# HG changeset patch
# User pimarin
# Date 1674482758 0
# Node ID c75629db91ff5e28935647a83c98d6c695d6b980
# Parent  63452ec27d36bb6f8dee20a8adc131ccb8493abf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 2479a339881bcd17ccefc0e13daab5b8f1e693af-dirty

diff -r 63452ec27d36 -r c75629db91ff bakta.xml
--- a/bakta.xml	Fri Jan 13 20:31:58 2023 +0000
+++ b/bakta.xml	Mon Jan 23 14:05:58 2023 +0000
@@ -58,6 +58,7 @@
         #if $annotation.translation_table
             --translation-table '$annotation.translation_table'
         #end if
+            --gram '?'
         $annotation.keep_contig_headers
         #if $annotation.replicons
             --replicons '$annotation.replicons'
@@ -93,7 +94,6 @@
             </param>
             <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
                 <options from_data_table="amrfinderplus_database">
-                    <column name="value" index="0"/>
                   <validator message="No amrfinderplus database is available" type="no_options"/>
                 </options>
             </param>
@@ -219,19 +219,18 @@
            <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
            <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
            <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
-          <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
-          <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
-          <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
-          <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
-          <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
-          <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
-          <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
-          <output name="annotation_plot">
+           <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
+           <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
+           <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
+           <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
+           <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
+           <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
+           <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
+           <output name="annotation_plot">
                <assert_contents>
                    <has_size value="418991" delta="1000"/>
                </assert_contents>
            </output>
-
           <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
           <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/>
        </test>
@@ -381,7 +380,7 @@
         1. You can specify if all sequences (chromosome or plasmids) are complete or not
         2. You can add your own prodigal training file for CDS predictionœ
         3. The translation table could be modified, default is the 11th for bacteria
-        4. You can specify if bacteria is gram -/+ or unknonw (not available in galaxy tool <= 1.6.1)
+        4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)
         5. You can keep the name of contig present in the input file
         6. You can specify your own replicon table as a TSV/CSV file
         7. The compliance option is for ready to submit annotation file to Public database
diff -r 63452ec27d36 -r c75629db91ff macro.xml
--- a/macro.xml	Fri Jan 13 20:31:58 2023 +0000
+++ b/macro.xml	Mon Jan 23 14:05:58 2023 +0000
@@ -1,6 +1,8 @@
 
 <macros>
     <token name="@TOOL_VERSION@">1.6.1</token>
+    <token name="@TOOL_VERSION@">1.6.1</token>
+    <token name="@TOOL_VERSION@">1.6.1</token>
     <token name="@BAKTA_VERSION@">1.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
diff -r 63452ec27d36 -r c75629db91ff test-data/amrfinderplus_database.loc
--- a/test-data/amrfinderplus_database.loc	Fri Jan 13 20:31:58 2023 +0000
+++ b/test-data/amrfinderplus_database.loc	Mon Jan 23 14:05:58 2023 +0000
@@ -4,5 +4,5 @@
 # value, name, path
 #
 # for example
-amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2    ${__HERE__}/amrfinderplus-db/2021-09-30.1
-amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	${__HERE__}/amrfinderplus-db/2021-09-30.1
+amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2	${__HERE__}/amrfinderplus-db/latest
+amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	${__HERE__}/amrfinderplus-db/latest