Update bakta to 1.6.0 and database options (#4947)

* add amrfinderplus_data_manager

* update bakta to 1.5.1 and also to filter the database depending of the tool version

* Revert "add amrfinderplus_data_manager"

This reverts commit 25a0413.

* try to solve the problem for test 1 and 4

* change bakta tool version 1.5 to 1.6.0

* add amrfinder select database

* update bakta to 1.6 and also test files

* remove the -r option for ln

* quote path

* Bump to 1.6.1

* Update from 1.6 to 1.6.1
Add the good database option for bakta and amrfinderplus
Update test output files
change the 'skip_analyse' code to implement suggestion of #echo " ".join($workflow.skip_analysis)

* update github link

* add line_diff option for all test files

* reset test-data

* make lines_diff as small as possible

* update bakta for plot output and to reduce number of output files

* Xremove tmp files

* update test files and output options

* remove tmp folder

* change option for plot

* reset files and use size assertions

Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: M Bernt <[email protected]>

tools/bakta/.shed.yml

@@ -5,7 +5,7 @@ long_description: |
   It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."
 categories:
 - Sequence Analysis
-remote_repository_url: "https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta"
+remote_repository_url: "https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta"
 homepage_url: "https://github.com/oschwengers/bakta"
 type: unrestricted
 auto_tool_repositories:

tools/bakta/macro.xml

@@ -1,5 +1,7 @@
+
 <macros>
-    <token name="@TOOL_VERSION@">1.5.0</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>
     <xml name="version_command">

tools/bakta/test-data/amrfinderplus_database.loc

@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, path
+#
+# for example
+amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2    ${__HERE__}/amrfinderplus-db
+amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	${__HERE__}/amrfinderplus-db

tools/bakta/test-data/bakta_database.loc

@@ -0,0 +1,11 @@
+# Tab separated with 4 columns:
+# value : unique value used to generate the database path provided from the zenodo DOI
+# dbkey : name of the database generate using the date and version of the bakta database
+# bakta_version : tool version to filter database version depending of the tool
+# path : final oath to bakta database on galaxy
+# value, dbkey, bakta_version, path
+# eg.
+# 7025248 V4.0_2022-08-29 1.5 path/to/db
+V0.0_date_test	7190015	1.5	${__HERE__}/test-db
+V0.1_2022-08-29	7197216	1.5	${__HERE__}/test-db
+V0.2_2022-08-19	7197217	1.7	${__HERE__}/test-db

tools/bakta/tool-data/amrfinderplus_database.loc.sample

@@ -0,0 +1,11 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, path
+#
+# for example
+2022-11-10_15:48    2022-10-11.2    ${__HERE__}
+amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2	/tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2
+amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	/tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1
+amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2	/tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2
+amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	/tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1

tools/bakta/tool-data/bakta_database.loc.sample

@@ -1,3 +1,3 @@
 #This is a sample file distributed with Galaxy that enables tools
 #file has this format (white space characters are TAB characters)
-test-db-bakta "Database test"	${__HERE__}/test-db
+#V4.0_2022-08-29	7025248	1.5	path/to/db

tools/bakta/tool_data_table_conf.xml.sample

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <table name="bakta_database" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, dbkey, bakta_version, path</columns>
         <file path="tool-data/bakta_database.loc.sample" />
     </table>
 </tables>

tools/bakta/tool_data_table_conf.xml.test

@@ -1,7 +1,11 @@
 <?xml version="1.0"?>
 <tables>
     <table name="bakta_database" comment_char="#">
+        <columns>value, dbkey, bakta_version, path</columns>
+        <file path="${__HERE__}/test-data/bakta_database.loc" />
+    </table>
+    <table name="amrfinderplus_database" comment_char="#">
         <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/test_database.loc" />
+        <file path="${__HERE__}/test-data/amrfinderplus_database.loc" />
     </table>
 </tables>