Merge pull request galaxyproject#18996 from martenson/schema-cond

doc/source/admin/galaxy_options.rst

@@ -5659,6 +5659,3 @@
     to the user. Currently only affects s3fs file sources.
 :Default: ``60``
 :Type: int
-
-
-

lib/galaxy/config/sample/galaxy.yml.sample

@@ -191,7 +191,7 @@ gravity:
 
     # Routes file to monitor.
     # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
-    # ``interactivetools_map is set.
+    # ``interactivetools_map is set``.
     # sessions: database/interactivetools_map.sqlite
 
     # Include verbose messages in gx-it-proxy
@@ -3007,4 +3007,3 @@ galaxy:
   # but outdated contents might be displayed to the user. Currently only
   # affects s3fs file sources.
   #file_source_listings_expiry_time: 60
-

lib/galaxy/config/sample/tool_shed.yml.sample

@@ -54,6 +54,9 @@ tool_shed:
   # options.
   #whoosh_index_dir: database/toolshed_whoosh_indexes
 
+  # Cache directory for Pydantic model objects.
+  #model_cache_dir: database/model_cache
+
   # For searching repositories at /api/repositories:
   #repo_name_boost: 0.9
 
@@ -426,4 +429,3 @@ tool_shed:
   # The value of this option will be resolved with respect to
   # <config_dir>.
   #datatypes_config_file: datatypes_conf.xml
-

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -312,8 +312,6 @@ A generalisation for macro tokens, templates and xml macros, i.e.
 `<macro name="an_xml_macro" type="xml">` is identical to `<xml name="an_xml_macro">`,
 `<macro name="a_template" type="template">` is identical to `<template name="a_template">`, and
 `<macro name="a_token" type="xml">` is identical to `<token name="a_token">`.
-
-Note that 
        ]]></xs:documentation>
         </xs:annotation>
       </xs:element>
@@ -3499,9 +3497,13 @@ Data source HTTP action (e.g. ``get`` or ``put``) to use.</xs:documentation>
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
 
-This is a container for conditional parameters in the tool (must contain 'when'
-tag sets) - the command line (or portions thereof) are then wrapped in an if-else
-statement. A good example tool that demonstrates many conditional parameters is
+This is a container for conditional parameters in the tool (must contain ``when``
+tag sets) - the command line is then wrapped in an if-else statement.
+
+Note that value of a conditional cannot be changed on the workflow run form.
+If you expect users to interact with the element during runtime consider using ``sections`` instead.
+
+An example tool that demonstrates conditional parameters is
 [biom_convert.xml](https://github.com/galaxyproject/tools-iuc/blob/main/tools/biom_format/biom_convert.xml).
 
 ```xml
@@ -3608,7 +3610,7 @@ Referenced parameter to pass method.]]></xs:documentation>
           <xs:annotation>
             <xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
 
-Is referenced parameter is the same group.]]></xs:documentation>
+Is referenced parameter in the same group.]]></xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="label" type="xs:string">
@@ -6286,7 +6288,7 @@ Therefore a filter for such a variable looks like the following example.
         <xs:documentation xml:lang="en"><![CDATA[
         A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements.
         `SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either
-        `lexical` or `numeric`. Default is lexical sorting by filename. 
+        `lexical` or `numeric`. Default is lexical sorting by filename.
         Note that lexical sorting is case sensitive, i.e. upper case characters come before lower case characters (e.g. "Apple" < "Banana" < "apple" < "banana").
         ]]></xs:documentation>
       </xs:annotation>