Mercurial > repos > rplanel > data_manager_defense_finder

changeset 2:6dd2220e0a1c draft

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planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/data_managers/data_manager_defense_finder commit b563c99a584471da6fe88c080f9bf8cdb219409f
author pasteur
date Thu, 13 Feb 2025 14:36:45 +0000
parents e661b9ac3223
children 46528ab18f85
files data_manager/data_manager_defense_finder.xml data_manager/defense_finder_models_fetcher.py data_manager_conf.xml test-data/defense_finder_test_data_manager.json tool-data/defense-finder.2.loc.sample tool-data/defense-finder.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 8 files changed, 33 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_defense_finder.xml	Wed Oct 11 07:33:01 2023 +0000
+++ b/data_manager/data_manager_defense_finder.xml	Thu Feb 13 14:36:45 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="defense_finder_models_fetcher_data_manager" name="DefenseFinder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0">
     <description>genotype data fetcher</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@TOOL_VERSION@">2.0.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">defense-finder</requirement>
@@ -11,19 +11,26 @@
     ]]></command>
     <inputs>
         <param name="model_version" type="text" label="Defense finder models version" help="The available versions can be found at : https://github.com/mdmparis/defense-finder-models/releases"/>
+        <param name="software_compatibility" type="text" label="List of defenseFinder versions compatibility" help="Enter the list of defenseFinder software versions that are compatible with the current model (e.g., 1.2.0,1.3.0,2.0.0). Separate multiple versions with commas if required."/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
     </outputs>
     <tests>
         <test>
-            <param name="model_version" value="1.2.3"/>
+            <param name="model_version" value="2.0.2"/>
+            <param name="software_compatibility" value="2.0.0"/>
             <output name="out_file" value="defense_finder_test_data_manager.json"/>
         </test>
     </tests>
     <help><![CDATA[
 Download Defense Finder models : https://github.com/mdmparis/defense-finder-models/
 check out the defense finder models versions from https://github.com/mdmparis/defense-finder-models/releases
+
+
+Starting from models version 2.0.0, only DefenseFinder version 2.0.0 is comaptible.
+
+
     ]]></help>
     <citations>
         <citation type="doi">10.1038/s41467-022-30269-9</citation>
--- a/data_manager/defense_finder_models_fetcher.py	Wed Oct 11 07:33:01 2023 +0000
+++ b/data_manager/defense_finder_models_fetcher.py	Thu Feb 13 14:36:45 2025 +0000
@@ -12,6 +12,7 @@
     dataset_basename = "defense-finder-models"
     models_version = args.version
     output_file = args.output
+    compat_version = args.compat_version
     dataset_value = f"{dataset_basename}_{models_version}"
     with open(output_file) as fh:
         params = json.load(fh)
@@ -35,9 +36,10 @@
         value=dataset_value,
         dbkey=dataset_basename,
         version=models_version,
-        name=f"Defense Finder models (version {models_version})",
+        name=f"version {models_version}",
         description="MacSyFinder models allowing for a systematic search of anti-phage systems",
         path=dataset_value,
+        compatibility_version=compat_version,
     )
 
     data_manager_json = dict(data_tables={"defense-finder": data_table_entry})
@@ -53,7 +55,14 @@
     parser = argparse.ArgumentParser(description="Create data manager json.")
     parser.add_argument("--out", dest="output", action="store", help="JSON filename")
     parser.add_argument(
-        "--version", dest="version", action="store", default="1", help="dataset version"
+        "--version", dest="version", action="store", default="1", help="model version"
+    )
+    parser.add_argument(
+        "--soft-compat-version",
+        dest="compat_version",
+        action="store",
+        default="2.0.0",
+        help="Which version of DefenseFinder is compatible with these models",
     )
 
     args = parser.parse_args()
--- a/data_manager_conf.xml	Wed Oct 11 07:33:01 2023 +0000
+++ b/data_manager_conf.xml	Thu Feb 13 14:36:45 2025 +0000
@@ -8,6 +8,7 @@
                 <column name="dbkey" />
                 <column name="name" />
                 <column name="version" />
+                <column name="compatibility_version" />
                 <column name="description" />
                 <column name="path" output_ref="out_file">
                     <move type="directory" relativize_symlinks="True">
--- a/test-data/defense_finder_test_data_manager.json	Wed Oct 11 07:33:01 2023 +0000
+++ b/test-data/defense_finder_test_data_manager.json	Thu Feb 13 14:36:45 2025 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"defense-finder": {"dbkey": "defense-finder-models", "description": "MacSyFinder models allowing for a systematic search of anti-phage systems", "name": "Defense Finder models (version 1.2.3)", "path": "defense-finder-models_1.2.3", "value": "defense-finder-models_1.2.3", "version": "1.2.3"}}}
\ No newline at end of file
+{"data_tables": {"defense-finder": {"compatibility_version": "2.0.0", "dbkey": "defense-finder-models", "description": "MacSyFinder models allowing for a systematic search of anti-phage systems", "name": "version 2.0.2", "path": "defense-finder-models_2.0.2", "value": "defense-finder-models_2.0.2", "version": "2.0.2"}}}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/defense-finder.2.loc.sample	Thu Feb 13 14:36:45 2025 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of defense finder models
+#
+# the columns are:
+# value, dbkey, name, version, description, path
+#
+# for example
+# defense-finder-models_1.2.2	defense-finder-models	Defense Finder models (version 1.2.2)	1.2.2	MacSyFinder models allowing for a systematic search of anti-phage systems	/depot/data/galaxy/defense-finder/defense-finder-models_1.2.2
--- a/tool-data/defense-finder.loc.sample	Wed Oct 11 07:33:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of defense finder models
-#
-# the columns are:
-# value, dbkey, name, version, description, path
-#
-# for example
-# defense-finder-models_1.2.2	defense-finder-models	Defense Finder models (version 1.2.2)	1.2.2	MacSyFinder models allowing for a systematic search of anti-phage systems	/depot/data/galaxy/defense-finder/defense-finder-models_1.2.2
--- a/tool_data_table_conf.xml.sample	Wed Oct 11 07:33:01 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Feb 13 14:36:45 2025 +0000
@@ -1,6 +1,6 @@
 <tables>
     <table name="defense-finder" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, version, description, path</columns>
-        <file path="tool-data/defense-finder.loc.sample" />
+        <columns>value, dbkey, name, version, soft compatibility version, description, path</columns>
+        <file path="tool-data/defense-finder.2.loc.sample" />
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Wed Oct 11 07:33:01 2023 +0000
+++ b/tool_data_table_conf.xml.test	Thu Feb 13 14:36:45 2025 +0000
@@ -1,6 +1,6 @@
 <tables>
     <table name="defense-finder" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, version, description, path</columns>
-        <file path="${__HERE__}/test-data/defense-finder.loc" />
+        <columns>value, dbkey, name, version, soft compatibility version, description, path</columns>
+        <file path="${__HERE__}/test-data/defense-finder.2.loc" />
     </table>
 </tables>
\ No newline at end of file