Rebase

lib/galaxy/tools/xsd/README.md

@@ -41,5 +41,5 @@ This code is free software released under the terms of the MIT license.
 # See also:
 
 * Galaxy https://usegalaxy.org/
-* Galaxy Tool XML File https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
+* Galaxy Tool XML File https://galaxyproject.org/admin/tools/tool-config-syntax/
 

lib/galaxy/tools/xsd/galaxy.xsd

@@ -166,8 +166,8 @@ graphical tool form by setting this to ``false``.</xs:documentation>
           <xs:documentation xml:lang="en">Allows for certain framework
 functionality to be performed on certain types of tools. Normal tools that execute
 typical command-line jobs do not need to specify this, special kinds of tools such
-as [Data Source](https://wiki.galaxyproject.org/Admin/Internals/DataSources) and
-[Data Manager](https://wiki.galaxyproject.org/Admin/Tools/DataManagers) tools should
+as [Data Source](https://galaxyproject.org/admin/internals/data-sources/) and
+[Data Manager](https://galaxyproject.org/admin/tools/data-managers/) tools should
 set this to have values such as ``data_source`` or ``manage_data``.</xs:documentation>
         </xs:annotation>
       </xs:attribute>
@@ -237,7 +237,7 @@ programs or modules that the tool depends upon are included in this tag set.
 When a tool runs, Galaxy attempts to *resolve* these requirements (also called
 dependencies). ``requirement``s are meant to be abstract and resolvable by
 multiple different systems (e.g. [conda](http://conda.pydata.org/docs/), the
-[Galaxy Tool Shed dependency management system](https://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
+[Galaxy Tool Shed dependency management system](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
 or [environment modules](http://modules.sourceforge.net/)).
 
 Read more about dependency resolvers in Galaxy on
@@ -251,7 +251,7 @@ discussed in greater detail
 This example shows a tool that requires the samtools 0.0.18 package.
 
 This package is available via the Tool Shed (see
-[Tool Shed dependency management](https://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories)
+[Tool Shed dependency management](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories)
 ) as well as [Conda](https://docs.galaxyproject.org/en/master/admin/conda_faq.html)
 and can be configured locally to adapt to any other package management system.
 
@@ -301,7 +301,7 @@ this tag allows the tool to suggest possible valid Docker containers for this
 tool.
 
 Read more about configuring Galaxy to run Docker jobs
-[here](https://wiki.galaxyproject.org/Admin/Tools/Docker).
+[here](https://galaxyproject.org/admin/tools/docker/).
 
 ]]></xs:documentation>
     </xs:annotation>
@@ -593,7 +593,7 @@ The documentation contained here is mostly reference documentation, for
 tutorials on writing tool tests please check out Planemo's
 [Test-Driven Development](https://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development)
 documentation or the much older wiki content for
-[WritingTests](https://wiki.galaxyproject.org/Admin/Tools/WritingTests).
+[WritingTests](https://galaxyproject.org/admin/tools/writing-tests/).
 
 ]]></xs:documentation>
     </xs:annotation>
@@ -1717,7 +1717,7 @@ conditionally reference ``${input_type.process_obs_metadata}`` with a Cheetah
 
 A common use of the conditional wrapper is to select between reference data
 managed by the Galaxy admins (for instance via
-[data managers](https://wiki.galaxyproject.org/Admin/Tools/DataManagers)
+[data managers](https://galaxyproject.org/admin/tools/data-managers/)
 ) and
 history files. A good example tool that demonstrates this is
 the [Bowtie 2](https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie2/bowtie2_wrapper.xml) wrapper.
@@ -3103,7 +3103,7 @@ specified by the ``skip`` attribute.</xs:documentation>
             <xs:documentation xml:lang="en">Tool data table name to check against
 if ``type`` is ``dataset_metadata_in_tool_data``. See the documentation for
 [tool data tables](https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables)
-and [data managers](https://wiki.galaxyproject.org/Admin/Tools/DataManagers) for
+and [data managers](https://galaxyproject.org/admin/tools/data-managers/) for
 more information.</xs:documentation>
           </xs:annotation>
         </xs:attribute>