# HG changeset patch
# User iuc
# Date 1691316725 0
# Node ID 2f40d2ccb0eb7a253055e837e214d0ab3c258961
# Parent  f05c3732764a0493c4c7885893bc818e0de51360
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31

diff -r f05c3732764a -r 2f40d2ccb0eb macros.xml
--- a/macros.xml	Wed Mar 22 18:05:47 2023 +0000
+++ b/macros.xml	Sun Aug 06 10:12:05 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.2.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="biotools">
         <xrefs>
@@ -33,8 +33,8 @@
         </citations>
     </xml>
     <xml name="creator">
-    <creator>
-        <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
-    </creator>
+        <creator>
+            <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
+        </creator>
     </xml>
 </macros>
diff -r f05c3732764a -r 2f40d2ccb0eb pharokka.xml
--- a/pharokka.xml	Wed Mar 22 18:05:47 2023 +0000
+++ b/pharokka.xml	Sun Aug 06 10:12:05 2023 +0000
@@ -1,6 +1,6 @@
 <tool id="pharokka" name="pharokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
-        rapid standardised annotation tool for bacteriophage genomes and metagenomes
+        Rapid standardised annotation tool for bacteriophage genomes and metagenomes
     </description>
     <macros>
         <import>macros.xml</import>
@@ -43,9 +43,9 @@
     </command>
     <inputs>
         <!-- the genome -->
-        <param type="data" name="fasta" format="fasta" help="Please upload an genome file of a bacteriophage in fasta format." label="Bacteriophage genome" />
+        <param type="data" name="fasta" format="fasta" help="Please upload a genome file of a bacteriophage in fasta format." label="Bacteriophage genome" />
         <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB">
-            <options from_data_table="pharokka_db">
+            <options from_data_table="pharokka_db_versioned">
             </options>
             <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." />
         </param>
@@ -57,7 +57,7 @@
                 Prodigal
             </option>
         </param>
-        <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="meta mode for metavirome input samples" />
+        <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="Meta mode for metavirome input samples" />
         <param name="evalue" type="float" value="1E-5" min="1E-20" max="10" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." />
         <!-- optional arguments -->
         <conditional name="terminase">
diff -r f05c3732764a -r 2f40d2ccb0eb test-data/pharokka_db.loc
--- a/test-data/pharokka_db.loc	Wed Mar 22 18:05:47 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-pharokka_db	pharokka_db	Minimal DB for testing	${__HERE__}/subset_pharokka_db
diff -r f05c3732764a -r 2f40d2ccb0eb test-data/pharokka_db_versioned.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pharokka_db_versioned.loc	Sun Aug 06 10:12:05 2023 +0000
@@ -0,0 +1,1 @@
+pharokka_db	pharokka_db	v0.1	Minimal DB for testing	${__HERE__}/subset_pharokka_db
diff -r f05c3732764a -r 2f40d2ccb0eb tool-data/pharokka_db.loc.sample
--- a/tool-data/pharokka_db.loc.sample	Wed Mar 22 18:05:47 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a pharokka DB folder. The pharokka_db.loc 
-#file needs this format (longer white space is the TAB character):
-
-#<unique_build_id>		<dbkey>		<display_name>		<DB_folder_path>
-
-# for example:
-
-# pharokka_db	pharokka_db	Pharokka Database v1.2.0	/data/pharokka_db
-
-# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or
-# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023)
\ No newline at end of file
diff -r f05c3732764a -r 2f40d2ccb0eb tool-data/pharokka_db_versioned.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pharokka_db_versioned.loc.sample	Sun Aug 06 10:12:05 2023 +0000
@@ -0,0 +1,12 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a pharokka DB folder. The pharokka_db.loc 
+#file needs this format (longer white space is the TAB character):
+
+#<unique_build_id>  <dbkey> <version>   <display_name>  <DB_folder_path>
+
+# for example:
+
+# pharokka_db	pharokka_db	v1.2.0	Pharokka Database v1.2.0	/data/pharokka_db
+
+# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or
+# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023)
\ No newline at end of file
diff -r f05c3732764a -r 2f40d2ccb0eb tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Mar 22 18:05:47 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Aug 06 10:12:05 2023 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of pharokka DB file -->
-    <table name="pharokka_db" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/pharokka_db.loc" />
+    <table name="pharokka_db_versioned" comment_char="#">
+        <columns>value, dbkey, version, name, path</columns>
+        <file path="tool-data/pharokka_db_versioned.loc" />
     </table>
 </tables>
\ No newline at end of file
diff -r f05c3732764a -r 2f40d2ccb0eb tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Wed Mar 22 18:05:47 2023 +0000
+++ b/tool_data_table_conf.xml.test	Sun Aug 06 10:12:05 2023 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of pharokka DB file -->
-    <table name="pharokka_db" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="${__HERE__}/test-data/pharokka_db.loc" />
+    <table name="pharokka_db_versioned" comment_char="#">
+        <columns>value, dbkey, version, name, path</columns>
+        <file path="${__HERE__}/test-data/pharokka_db_versioned.loc" />
     </table>
 </tables>
\ No newline at end of file