Mercurial > repos > estrain > data_manager_amrfinderplus

changeset 1:041f234a2d77 draft default tip

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planemo upload commit d4704f3c30eb441ff55cd913dfdc1c55197da3b1
author galaxytrakr
date Fri, 13 Nov 2026 12:16:08 +0000
parents 2986b488a62b
children
files data_manager/data_manager_amrfinderplus.xml test-data/amrfinderplus_versioned.loc.test tool-data/amrfinderplus_versioned.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 5 files changed, 34 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_amrfinderplus.xml	Thu Mar 12 19:41:57 2026 +0000
+++ b/data_manager/data_manager_amrfinderplus.xml	Fri Nov 13 12:16:08 2026 +0000
@@ -1,7 +1,8 @@
-<tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="4.2.5" profile="20.03">
+<tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="4.2.7" profile="20.03">
     <requirements>
-        <requirement type="package" version="4.2.5">ncbi-amrfinderplus</requirement>
+        <requirement type="package" version="4.2.7">ncbi-amrfinderplus</requirement>
         <requirement type="package" version="3.10.6">python</requirement>
+        
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       python '$__tool_directory__/data_manager_amrfinderplus.py' '$output_file'
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus_versioned.loc.test	Fri Nov 13 12:16:08 2026 +0000
@@ -0,0 +1,10 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, db_version, path
+#
+# for example
+amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 amrfinderplus-db
+amrfinderplus_V3.12_2024-01-31.1 V3.12-2024-01-31.1 3.12 amrfinderplus-db
+amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 /private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2
+amrfinderplus_V3.12_2024-01-31.1 V3.12-2024-01-31.1 3.12 /private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-01-31.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/amrfinderplus_versioned.loc	Fri Nov 13 12:16:08 2026 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, db_version, path
+#
+# for example
+#amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12    amrfinderplus-db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Nov 13 12:16:08 2026 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of amrfinderplus database in the required format -->
+    <table name="amrfinderplus_versioned_database" comment_char="#">
+        <columns>value, name, db_version, path</columns>
+        <file path="tool-data/amrfinderplus_versioned.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Nov 13 12:16:08 2026 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of amrfinderplus database in the required format -->
+    <table name="amrfinderplus_versioned_database" comment_char="#">
+        <columns>value, name, db_version, path</columns>
+        <file path="${__HERE__}/test-data/amrfinderplus_versioned.loc.test"/>
+    </table>
+</tables>