galaxyproject · mvdbeek · Nov 1, 2023 · Oct 30, 2023 · Oct 31, 2023 · Oct 31, 2023
diff --git a/docs/commands.rst b/docs/commands.rst
@@ -68,4 +68,5 @@ documentation describes these commands.
 .. include:: commands/workflow_job_init.rst
 .. include:: commands/workflow_lint.rst
 .. include:: commands/workflow_test_init.rst
+.. include:: commands/workflow_test_on_invocation.rst
 .. include:: commands/workflow_upload.rst
diff --git a/docs/commands/autoupdate.rst b/docs/commands/autoupdate.rst
@@ -1,6 +1,6 @@
 
 ``autoupdate`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``autoupdate``. This help message can be generated with ``planemo autoupdate
@@ -32,15 +32,15 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
                                       tools and workflows. Defaults to a local
                                       Galaxy, but running Galaxy within a Docker
                                       container.
-      --update_test_data              Update test-data directory with job outputs
-                                      (normally written to directory
-                                      --job_output_files if specified.)
       --paste_test_data_paths / --no_paste_test_data_paths
                                       By default Planemo will use or not use
                                       Galaxy's path paste option to load test data
                                       into a history based on the engine type it is
                                       targeting. This can override the logic to
                                       explicitly enable or disable path pasting.
+      --update_test_data              Update test-data directory with job outputs
+                                      (normally written to directory
+                                      --job_output_files if specified.)
       --test_output PATH              Output test report (HTML - for humans)
                                       defaults to tool_test_output.html.
       --test_output_text PATH         Output test report (Basic text - for display

diff --git a/docs/commands/ci_find_repos.rst b/docs/commands/ci_find_repos.rst
@@ -1,6 +1,6 @@
 
 ``ci_find_repos`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``ci_find_repos``. This help message can be generated with ``planemo ci_find_repos

diff --git a/docs/commands/ci_find_tools.rst b/docs/commands/ci_find_tools.rst
@@ -1,6 +1,6 @@
 
 ``ci_find_tools`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``ci_find_tools``. This help message can be generated with ``planemo ci_find_tools

diff --git a/docs/commands/ci_setup.rst b/docs/commands/ci_setup.rst
@@ -1,6 +1,6 @@
 
 ``ci_setup`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``ci_setup``. This help message can be generated with ``planemo ci_setup

diff --git a/docs/commands/clone.rst b/docs/commands/clone.rst
@@ -1,6 +1,6 @@
 
 ``clone`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``clone``. This help message can be generated with ``planemo clone

diff --git a/docs/commands/conda_build.rst b/docs/commands/conda_build.rst
@@ -1,6 +1,6 @@
 
 ``conda_build`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``conda_build``. This help message can be generated with ``planemo conda_build

diff --git a/docs/commands/conda_env.rst b/docs/commands/conda_env.rst
@@ -1,6 +1,6 @@
 
 ``conda_env`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``conda_env``. This help message can be generated with ``planemo conda_env

diff --git a/docs/commands/conda_init.rst b/docs/commands/conda_init.rst
@@ -1,6 +1,6 @@
 
 ``conda_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``conda_init``. This help message can be generated with ``planemo conda_init

diff --git a/docs/commands/conda_install.rst b/docs/commands/conda_install.rst
@@ -1,6 +1,6 @@
 
 ``conda_install`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``conda_install``. This help message can be generated with ``planemo conda_install

diff --git a/docs/commands/conda_search.rst b/docs/commands/conda_search.rst
@@ -1,6 +1,6 @@
 
 ``conda_search`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``conda_search``. This help message can be generated with ``planemo conda_search

diff --git a/docs/commands/config_init.rst b/docs/commands/config_init.rst
@@ -1,6 +1,6 @@
 
 ``config_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``config_init``. This help message can be generated with ``planemo config_init

diff --git a/docs/commands/container_register.rst b/docs/commands/container_register.rst
@@ -1,6 +1,6 @@
 
 ``container_register`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``container_register``. This help message can be generated with ``planemo container_register

diff --git a/docs/commands/create_alias.rst b/docs/commands/create_alias.rst
@@ -1,6 +1,6 @@
 
 ``create_alias`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``create_alias``. This help message can be generated with ``planemo create_alias

diff --git a/docs/commands/database_create.rst b/docs/commands/database_create.rst
@@ -1,6 +1,6 @@
 
 ``database_create`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``database_create``. This help message can be generated with ``planemo database_create

diff --git a/docs/commands/database_delete.rst b/docs/commands/database_delete.rst
@@ -1,6 +1,6 @@
 
 ``database_delete`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``database_delete``. This help message can be generated with ``planemo database_delete

diff --git a/docs/commands/database_list.rst b/docs/commands/database_list.rst
@@ -1,6 +1,6 @@
 
 ``database_list`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``database_list``. This help message can be generated with ``planemo database_list

diff --git a/docs/commands/delete_alias.rst b/docs/commands/delete_alias.rst
@@ -1,6 +1,6 @@
 
 ``delete_alias`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``delete_alias``. This help message can be generated with ``planemo delete_alias

diff --git a/docs/commands/docker_build.rst b/docs/commands/docker_build.rst
@@ -1,6 +1,6 @@
 
 ``docker_build`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``docker_build``. This help message can be generated with ``planemo docker_build

diff --git a/docs/commands/docker_shell.rst b/docs/commands/docker_shell.rst
@@ -1,6 +1,6 @@
 
 ``docker_shell`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``docker_shell``. This help message can be generated with ``planemo docker_shell

diff --git a/docs/commands/dockstore_init.rst b/docs/commands/dockstore_init.rst
@@ -1,6 +1,6 @@
 
 ``dockstore_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``dockstore_init``. This help message can be generated with ``planemo dockstore_init

diff --git a/docs/commands/docs.rst b/docs/commands/docs.rst
@@ -1,6 +1,6 @@
 
 ``docs`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``docs``. This help message can be generated with ``planemo docs

diff --git a/docs/commands/lint.rst b/docs/commands/lint.rst
@@ -1,6 +1,6 @@
 
 ``lint`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``lint``. This help message can be generated with ``planemo lint

diff --git a/docs/commands/list_alias.rst b/docs/commands/list_alias.rst
@@ -1,6 +1,6 @@
 
 ``list_alias`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``list_alias``. This help message can be generated with ``planemo list_alias

diff --git a/docs/commands/list_invocations.rst b/docs/commands/list_invocations.rst
@@ -1,6 +1,6 @@
 
 ``list_invocations`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``list_invocations``. This help message can be generated with ``planemo list_invocations

diff --git a/docs/commands/list_repos.rst b/docs/commands/list_repos.rst
@@ -1,6 +1,6 @@
 
 ``list_repos`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``list_repos``. This help message can be generated with ``planemo list_repos

diff --git a/docs/commands/merge_test_reports.rst b/docs/commands/merge_test_reports.rst
@@ -1,6 +1,6 @@
 
 ``merge_test_reports`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``merge_test_reports``. This help message can be generated with ``planemo merge_test_reports

diff --git a/docs/commands/mull.rst b/docs/commands/mull.rst
@@ -1,6 +1,6 @@
 
 ``mull`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``mull``. This help message can be generated with ``planemo mull

diff --git a/docs/commands/mulled_init.rst b/docs/commands/mulled_init.rst
@@ -1,6 +1,6 @@
 
 ``mulled_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``mulled_init``. This help message can be generated with ``planemo mulled_init

diff --git a/docs/commands/normalize.rst b/docs/commands/normalize.rst
@@ -1,6 +1,6 @@
 
 ``normalize`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``normalize``. This help message can be generated with ``planemo normalize

diff --git a/docs/commands/open.rst b/docs/commands/open.rst
@@ -1,6 +1,6 @@
 
 ``open`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``open``. This help message can be generated with ``planemo open

diff --git a/docs/commands/profile_create.rst b/docs/commands/profile_create.rst
@@ -1,6 +1,6 @@
 
 ``profile_create`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``profile_create``. This help message can be generated with ``planemo profile_create

diff --git a/docs/commands/profile_delete.rst b/docs/commands/profile_delete.rst
@@ -1,6 +1,6 @@
 
 ``profile_delete`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``profile_delete``. This help message can be generated with ``planemo profile_delete

diff --git a/docs/commands/profile_list.rst b/docs/commands/profile_list.rst
@@ -1,6 +1,6 @@
 
 ``profile_list`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``profile_list``. This help message can be generated with ``planemo profile_list

diff --git a/docs/commands/project_init.rst b/docs/commands/project_init.rst
@@ -1,6 +1,6 @@
 
 ``project_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``project_init``. This help message can be generated with ``planemo project_init

diff --git a/docs/commands/pull_request.rst b/docs/commands/pull_request.rst
@@ -1,6 +1,6 @@
 
 ``pull_request`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``pull_request``. This help message can be generated with ``planemo pull_request

diff --git a/docs/commands/rerun.rst b/docs/commands/rerun.rst
@@ -1,6 +1,6 @@
 
 ``rerun`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``rerun``. This help message can be generated with ``planemo rerun

diff --git a/docs/commands/run.rst b/docs/commands/run.rst
@@ -1,6 +1,6 @@
 
 ``run`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``run``. This help message can be generated with ``planemo run
@@ -212,15 +212,15 @@ Planemo command for running tools and jobs.
                                       created.
       --no_wait                       After invoking a job or workflow, do not wait
                                       for completion.
-      --update_test_data              Update test-data directory with job outputs
-                                      (normally written to directory
-                                      --job_output_files if specified.)
       --paste_test_data_paths / --no_paste_test_data_paths
                                       By default Planemo will use or not use
                                       Galaxy's path paste option to load test data
                                       into a history based on the engine type it is
                                       targeting. This can override the logic to
                                       explicitly enable or disable path pasting.
+      --update_test_data              Update test-data directory with job outputs
+                                      (normally written to directory
+                                      --job_output_files if specified.)
       --test_output PATH              Output test report (HTML - for humans)
                                       defaults to tool_test_output.html.
       --test_output_text PATH         Output test report (Basic text - for display

diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst
@@ -1,6 +1,6 @@
 
 ``serve`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``serve``. This help message can be generated with ``planemo serve

diff --git a/docs/commands/share_test.rst b/docs/commands/share_test.rst
@@ -1,6 +1,6 @@
 
 ``share_test`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``share_test``. This help message can be generated with ``planemo share_test

diff --git a/docs/commands/shed_build.rst b/docs/commands/shed_build.rst
@@ -1,6 +1,6 @@
 
 ``shed_build`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``shed_build``. This help message can be generated with ``planemo shed_build

diff --git a/docs/commands/shed_create.rst b/docs/commands/shed_create.rst
@@ -1,6 +1,6 @@
 
 ``shed_create`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``shed_create``. This help message can be generated with ``planemo shed_create

diff --git a/docs/commands/shed_diff.rst b/docs/commands/shed_diff.rst
@@ -1,6 +1,6 @@
 
 ``shed_diff`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``shed_diff``. This help message can be generated with ``planemo shed_diff

diff --git a/docs/commands/shed_init.rst b/docs/commands/shed_init.rst
@@ -1,6 +1,6 @@
 
 ``shed_init`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``shed_init``. This help message can be generated with ``planemo shed_init

diff --git a/docs/commands/shed_lint.rst b/docs/commands/shed_lint.rst
@@ -1,6 +1,6 @@
 
 ``shed_lint`` command
-======================================
+========================================
 
 This section is auto-generated from the help text for the planemo command
 ``shed_lint``. This help message can be generated with ``planemo shed_lint