Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

changeset 6:4e933a39094f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 3b2a82fa2ba8408609a72fefd18571223f080a6d
author pimarin
date Wed, 23 Aug 2023 08:23:25 +0000
parents 60cfd33bc2fb
children ed0f59ab5e61
files data_manager/plasmidfinder_fetch_database.xml data_manager_conf.xml test-data/plasmidfinder.loc.test tool-data/plasmidfinder_database.loc tool-data/plasmidfinder_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 7 files changed, 14 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/plasmidfinder_fetch_database.xml	Mon Jul 24 10:00:33 2023 +0000
+++ b/data_manager/plasmidfinder_fetch_database.xml	Wed Aug 23 08:23:25 2023 +0000
@@ -9,7 +9,6 @@
         python '$__tool_directory__/plasmidfinder_fetch_database.py'
         --db_version '$database_select'
         '$output_file'
-        && cat '$output_file'
       ]]></command>
     <inputs>
         <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
--- a/data_manager_conf.xml	Mon Jul 24 10:00:33 2023 +0000
+++ b/data_manager_conf.xml	Wed Aug 23 08:23:25 2023 +0000
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <data_managers>
     <data_manager tool_file="data_manager/plasmidfinder_fetch_database.xml" id="plasmidfinder_fetch_database">
         <data_table name="plasmidfinder_database">
@@ -9,9 +8,9 @@
                 <column name="path" output_ref="output_file">
                     <move type="directory" relativize_symlinks="True">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plasmidfinder_database/${name}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plasmidfinder-db/${name}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plasmidfinder_database/${name}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plasmidfinder-db/${name}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/test-data/plasmidfinder.loc.test	Mon Jul 24 10:00:33 2023 +0000
+++ b/test-data/plasmidfinder.loc.test	Wed Aug 23 08:23:25 2023 +0000
@@ -1,9 +1,1 @@
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmptllq5k0r/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmpnshbzr8f/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmpgfqg6r8x/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmpam2pha1m/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmp_tzl62ye/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmpu0batsz4/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmp72f81ayd/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmp73run5j6/galaxy-dev/tool-data/plasmidfinder_database/2.1_2019_08_28
-plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	/tmp/tmpngljkg08/galaxy-dev/tool-data/plasmidfinder_database/2.1_2019_08_28
+plasmidfinder_1307168_2019_08_28	2.1_2019_08_28	2019_08_28	plasmidfinder-db
--- a/tool-data/plasmidfinder_database.loc	Mon Jul 24 10:00:33 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-# this is a tab separated file describing the location of plasmidfinder database
-# The name was obtained by merging date of download and commit number
-# the columns are:
-# value, name, date, path
-#
-# for example
-#plasmidfinder_9002e7282dd0_2022-12-20	9002e7282dd0_2022-12-20	2022-12-20	plasmidfinder-db
-#plasmidfinder_1307168b1ce7_2022-12-20	2.1_2022-12-20	2022-12-20	plasmidfinder-db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/plasmidfinder_database.loc.sample	Wed Aug 23 08:23:25 2023 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of plasmidfinder database
+# The name was obtained by merging date of download and commit number
+# the columns are:
+# value, name, date, path
+#
+# for example
+#plasmidfinder_9002e7282dd0_2022-12-20	9002e7282dd0_2022-12-20	2022-12-20	plasmidfinder-db
+#plasmidfinder_1307168b1ce7_2022-12-20	2.1_2022-12-20	2022-12-20	plasmidfinder-db
--- a/tool_data_table_conf.xml.sample	Mon Jul 24 10:00:33 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Aug 23 08:23:25 2023 +0000
@@ -3,6 +3,6 @@
     <!-- Locations of plasmidfinder database in the required format -->
     <table name="plasmidfinder_database" comment_char="#">
         <columns>value, name, date, path</columns>
-        <file path="tool-data/plasmidfinder.loc" />
+        <file path="tool-data/plasmidfinder_database.loc.sample" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Mon Jul 24 10:00:33 2023 +0000
+++ b/tool_data_table_conf.xml.test	Wed Aug 23 08:23:25 2023 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of plasmidfinder database in the required format -->
-    <table name="plasmidfinder_database" comment_char="#">
-        <columns>value, name, date,  path</columns>
+    <table name="plasmidfinder_database" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, date, path</columns>
         <file path="${__HERE__}/test-data/plasmidfinder.loc.test"/>
     </table>
 </tables>