# HG changeset patch
# User tduigou
# Date 1759415251 0
# Node ID 815748762646f925cf2db58ec0211b5743857211
# Parent  95b4196b4dedc9e8a39e8b69bdd72d42d45c9263
planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5

diff -r 95b4196b4ded -r 815748762646 generate_test.py
--- a/generate_test.py	Mon Sep 15 12:59:58 2025 +0000
+++ b/generate_test.py	Thu Oct 02 14:27:31 2025 +0000
@@ -49,7 +49,7 @@
     cmd = ["--input-template-id-str", template_id]
     value = run_cmd(subcommand="templates-summary", sub_cmd=cmd)
     print("Test:", " ".join(cmd), "md5:", value)
-    
+
     print("=" * 50)
 
     print("templates-sources")
@@ -57,9 +57,9 @@
     cmd = ["--input-template-id-str", template_id]
     value = run_cmd(subcommand="templates-sources", sub_cmd=cmd)
     print("Test:", " ".join(cmd), "md5:", value)
-    
+
     print("=" * 50)
-    
+
     print("templates-count")
     smarts_str = "[O]-[C](=[O])"
     cmd = ["--input-smarts-str", smarts_str]
@@ -73,4 +73,4 @@
     cmd = ["--input-smarts-str", smarts_str]
     value = run_cmd(subcommand="templates-export", sub_cmd=cmd)
     print("Test:", " ".join(cmd), "md5:", value)
-    """
\ No newline at end of file
+    """
diff -r 95b4196b4ded -r 815748762646 query.py
--- a/query.py	Mon Sep 15 12:59:58 2025 +0000
+++ b/query.py	Thu Oct 02 14:27:31 2025 +0000
@@ -17,11 +17,11 @@
     chemical_domain_str: str,
     ec_number_str: str,
     min_radius_int: int,
-    valid_str: str,    
+    valid_str: str,
     dedup_str: str,
     limit_int: int,
     offset_int: int,
-    ) -> Tuple:
+) -> Tuple:
     url = f"{BASE_URL}/templates"
     params = []
     if smarts_str:
@@ -48,16 +48,19 @@
         params.append(("offset", str(offset_int)))
     return url, params
 
+
 def from_templates_summary(template_id_str: str) -> Tuple:
     url = f"{BASE_URL}/templates/{template_id_str}/summary"
     params = {}
     return url, params
 
+
 def from_templates_sources(template_id_str: str) -> Tuple:
     url = f"{BASE_URL}/templates/{template_id_str}/sources"
     params = {}
     return url, params
 
+
 def from_templates_count(
     smarts_str: str,
     template_ids_str: str,
@@ -66,9 +69,9 @@
     chemical_domain_str: str,
     ec_number_str: str,
     min_radius_int: int,
-    valid_str: str,    
+    valid_str: str,
     dedup_str: str,
-    ) -> Tuple:
+) -> Tuple:
     url = f"{BASE_URL}/templates_count"
     params = []
     if smarts_str:
@@ -91,6 +94,7 @@
         params.append(("dedup", dedup_str))
     return url, params
 
+
 def from_templates_export(
     generation_token_str: str,
     smarts_str: str,
@@ -100,9 +104,9 @@
     chemical_domain_str: str,
     ec_number_str: str,
     min_radius_int: int,
-    valid_str: str,    
+    valid_str: str,
     dedup_str: str,
-    ) -> Tuple:
+) -> Tuple:
     url = f"{BASE_URL}/templates_export"
     params = []
     if generation_token_str:
@@ -127,19 +131,23 @@
         params.append(("dedup", dedup_str))
     return url, params
 
+
 def query(url: str, params: Dict):
     response = requests.get(url, params=params)
     response.raise_for_status()
     return response
 
+
 def write_json(path: str, data: Dict):
     with open(path, "w") as fd:
         json.dump(data, fd, indent=4)
 
+
 def write_tab(path: str, data: str):
     with open(path, "w") as fd:
         fd.write(data)
 
+
 def main():
     parser = argparse.ArgumentParser(
         description="Query RetroRules API via command-line endpoints."
@@ -215,7 +223,7 @@
         required=True,
         help="Path to output JSON file",
     )
-    
+
     # Subcommand: templates-sources
     parser_tem_sou = subparsers.add_parser("templates-sources", help="From templates-sources")
     parser_tem_sou.add_argument("--input-template-id-str", required=True, help="Template ID")
diff -r 95b4196b4ded -r 815748762646 retrorules.xml
--- a/retrorules.xml	Mon Sep 15 12:59:58 2025 +0000
+++ b/retrorules.xml	Thu Oct 02 14:27:31 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="retrorules" name="RetroRules" version="1.0+galaxy2" profile="21.09" license="MIT">
+<tool id="retrorules" name="RetroRules" version="1.0+galaxy3" profile="21.09" license="MIT">
     <description>Querying the RetroRules REST API</description>
     <requirements>
         <requirement type="package" version="2">requests</requirement>
@@ -166,7 +166,7 @@
                 <param name="smarts" value="[O]-[C](=[O])" />
                 <param name="limit" value="5" />
             </conditional>
-            <output name="output_json" md5="0e4a782a2868c4b85a96f7c1d4ecaef8" />
+            <output name="output_json" md5="e8655d2abbd9e3cc9ff140d93306efbe" />
         </test>
         <!-- Templates summary -->
         <test>
@@ -174,7 +174,7 @@
                 <param name="from_src" value="from_templates_summary" />
                 <param name="template_id" value="RR:03-27BC85-19184A-A71018" />
             </conditional>
-            <output name="output_json" md5="8cde1ac45b324c9893f70254587feb30" />
+            <output name="output_json" md5="5373a8046c866466c8bfb13ec7b9efff" />
         </test>
         <!-- Templates sources -->
         <test>
@@ -182,7 +182,7 @@
                 <param name="from_src" value="from_templates_sources" />
                 <param name="template_id" value="RR:03-27BC85-19184A-A71018" />
             </conditional>
-            <output name="output_json" md5="33768abfc48aa896bfdfb736a3001950" />
+            <output name="output_json" md5="d4d9a63e18ca8c2a7a07590b3b6f7476" />
         </test>
         <!-- Templates count -->
         <test>