diff --git a/docs/commands/lint.rst b/docs/commands/lint.rst index f07737a34..16d5a3bff 100644 --- a/docs/commands/lint.rst +++ b/docs/commands/lint.rst @@ -23,8 +23,7 @@ Check for common errors and best practices. (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. - --xsd / --no_xsd Include tool XSD validation in linting - process. + --skip_file FILE File containing a list of lint tests to skip -r, --recursive Recursively perform command for subdirectories. --urls Check validity of URLs in XML files diff --git a/docs/commands/run.rst b/docs/commands/run.rst index cffd9aa33..4b11b7692 100644 --- a/docs/commands/run.rst +++ b/docs/commands/run.rst @@ -212,8 +212,9 @@ Planemo command for running tools and jobs. --galaxy_user_key TEXT User key to use with external Galaxy engine. --history_name TEXT Name to give a Galaxy history, if one is created. - --history_id TEXT Do not create a new history. Send the results - of the run in the history with the provided ID. + --history_id TEXT Send the results of the run to the history + with the provided ID. A history with this ID + must exist. --no_wait After invoking a job or workflow, do not wait for completion. --paste_test_data_paths / --no_paste_test_data_paths diff --git a/docs/commands/shed_lint.rst b/docs/commands/shed_lint.rst index dd6604c26..1a0500100 100644 --- a/docs/commands/shed_lint.rst +++ b/docs/commands/shed_lint.rst @@ -38,10 +38,9 @@ help text for mentioned URLs and checks those. (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. + --skip_file FILE File containing a list of lint tests to skip --tools Lint tools discovered in the process of linting repositories. - --xsd / --no_xsd Include tool XSD validation in linting - process. --ensure_metadata Ensure .shed.yml files contain enough metadata for each repository to allow automated creation and/or updates. diff --git a/docs/commands/test.rst b/docs/commands/test.rst index 618c63a5d..c04feebd0 100644 --- a/docs/commands/test.rst +++ b/docs/commands/test.rst @@ -245,6 +245,9 @@ please careful and do not try this against production Galaxy instances. --galaxy_user_key TEXT User key to use with external Galaxy engine. --history_name TEXT Name to give a Galaxy history, if one is created. + --history_id TEXT Send the results of the run to the history + with the provided ID. A history with this ID + must exist. --no_wait After invoking a job or workflow, do not wait for completion. --help Show this message and exit. diff --git a/planemo/options.py b/planemo/options.py index 7e4ea8b3d..7ceff7de4 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -523,11 +523,12 @@ def history_name(): help="Name to give a Galaxy history, if one is created.", ) + def history_id(): return planemo_option( "--history_id", type=str, - help="Do not create a new history. Send the results of the run in the history with the provided ID.", + help="Send the results of the run to the history with the provided ID. A history with this ID must exist.", )