Mercurial > repos > iuc > data_manager_pharokka

changeset 1:50caca83e7c9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
author iuc
date Sun, 06 Aug 2023 10:11:42 +0000
parents 97f310b8e308
children
files data_manager/data_manager_fetch_pharokka_db.py data_manager/macros.xml data_manager/pharokka_db_fetcher.xml data_manager_conf.xml test-data/pharokka_db.loc tool-data/pharokka_db.loc tool-data/pharokka_db_versioned.loc.sample tool_data_table_conf.xml.sample
diffstat 8 files changed, 30 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_fetch_pharokka_db.py	Thu Apr 20 07:51:43 2023 +0000
+++ b/data_manager/data_manager_fetch_pharokka_db.py	Sun Aug 06 10:11:42 2023 +0000
@@ -60,7 +60,7 @@
     # Update Data Manager JSON and write to file
     data_manager_entry = {
         "data_tables": {
-            "pharokka_db": {
+            "pharokka_db_versioned": {
                 "value": db_value,
                 "dbkey": db_value,
                 "version": args.version,
--- a/data_manager/macros.xml	Thu Apr 20 07:51:43 2023 +0000
+++ b/data_manager/macros.xml	Sun Aug 06 10:11:42 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="biotools">
         <xrefs>
--- a/data_manager/pharokka_db_fetcher.xml	Thu Apr 20 07:51:43 2023 +0000
+++ b/data_manager/pharokka_db_fetcher.xml	Sun Aug 06 10:11:42 2023 +0000
@@ -1,12 +1,13 @@
 <?xml version="1.0"?>
 <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fetches the DB required for phrokka</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="biotools" />
     <expand macro="requirements" />
     <expand macro="version" />
-    <description>Fetches the DB required for phrokka</description>
+
     <command detect_errors="exit_code">
     <![CDATA[
         python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}' 
@@ -14,8 +15,10 @@
     ]]>
     </command>
     <inputs>
-    <param name="test_data_manager" type="hidden" value=""/>
-    <param argument="--version" type="text" value="v1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version."/>
+    <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />
+
+    <!-- <param name="test_data_manager" type="text" value=""/> -->
+    <param argument="--version" type="text" value="1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version. The default value is recommended."/>
     </inputs>
     <outputs>
         <data format="data_manager_json" name="out_file" />
@@ -35,6 +38,11 @@
     </test>
     </tests>
     <help>
+        <![CDATA[
+        Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
+        This data manager fetches the DB using the build-in tool download script.
+        The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102
+        ]]>
     </help>
     <expand macro="citations" />
     <expand macro="creator" />
--- a/data_manager_conf.xml	Thu Apr 20 07:51:43 2023 +0000
+++ b/data_manager_conf.xml	Sun Aug 06 10:11:42 2023 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <data_managers>
 
-    <data_manager tool_file="data_manager/pharokka_db_fetcher.xml" id="pharokka_db_fetcher" version="1.2">
-        <data_table name="pharokka_db">
+    <data_manager tool_file="data_manager/pharokka_db_fetcher.xml" id="pharokka_db_fetcher">
+        <data_table name="pharokka_db_versioned">
             <output>
                 <column name="value" />
                 <column name="dbkey" />
--- a/test-data/pharokka_db.loc	Thu Apr 20 07:51:43 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>	<version>	<display_name>	<DB_folder_path>
-
-# for example:
-
-# pharokka_db	pharokka_db v1.2.1	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
--- a/tool-data/pharokka_db.loc	Thu Apr 20 07:51:43 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>	<version>	<display_name>	<DB_folder_path>
-
-# for example:
-
-# pharokka_db	pharokka_db v1.2.1	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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pharokka_db_versioned.loc.sample	Sun Aug 06 10:11:42 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_versioned.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	v1.2.1	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
--- a/tool_data_table_conf.xml.sample	Thu Apr 20 07:51:43 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Aug 06 10:11:42 2023 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of pharokka DB file -->
-    <table name="pharokka_db" comment_char="#">
+    <table name="pharokka_db_versioned" comment_char="#">
         <columns>value, dbkey, version, name, path</columns>
-        <file path="tool-data/pharokka_db.loc" />
+        <file path="tool-data/pharokka_db_versioned.loc" />
     </table>
 </tables>
\ No newline at end of file