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Rebuild docs.
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@jmchilton
jmchilton committed May 23, 2018
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14 changes: 13 additions & 1 deletion docs/commands/run.rst
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Expand Up @@ -131,6 +131,12 @@ Planemo command for running tools and jobs.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--cwl Configure Galaxy for use with CWL tool. (this
option is experimental and will be replaced
when and if CWL support is merged into
Expand All @@ -149,7 +155,7 @@ Planemo command for running tools and jobs.
as tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container or the CWL reference implementation
'cwltool' and be selected.
'cwltool' and 'toil' be selected.
--non_strict_cwl Disable strict validation of CWL.
--no-container, --no_container If cwltool engine is used, disable Docker
container usage.
Expand All @@ -163,6 +169,12 @@ Planemo command for running tools and jobs.
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
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12 changes: 12 additions & 0 deletions docs/commands/serve.rst
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Expand Up @@ -158,6 +158,12 @@ Galaxy instance.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file PATH Location of pid file is executed with
--daemon.
Expand All @@ -166,6 +172,12 @@ Galaxy instance.
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--cwl Configure Galaxy for use with CWL tool. (this
option is experimental and will be replaced
when and if CWL support is merged into
Expand Down
6 changes: 6 additions & 0 deletions docs/commands/shed_serve.rst
View file
Expand Up @@ -155,6 +155,12 @@ logged into and explored interactively.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--pid_file PATH Location of pid file is executed with
--daemon.
--daemon Serve Galaxy process as a daemon.
Expand Down
14 changes: 13 additions & 1 deletion docs/commands/test.rst
View file
Expand Up @@ -151,6 +151,12 @@ please careful and do not try this against production Galaxy instances.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
Expand Down Expand Up @@ -180,7 +186,7 @@ please careful and do not try this against production Galaxy instances.
as tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container or the CWL reference implementation
'cwltool' and be selected.
'cwltool' and 'toil' be selected.
--non_strict_cwl Disable strict validation of CWL.
--no-container, --no_container If cwltool engine is used, disable Docker
container usage.
Expand All @@ -194,6 +200,12 @@ please careful and do not try this against production Galaxy instances.
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
Expand Down
12 changes: 12 additions & 0 deletions docs/commands/tool_factory.rst
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Expand Up @@ -143,6 +143,12 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file PATH Location of pid file is executed with
--daemon.
Expand All @@ -151,5 +157,11 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011.
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.
12 changes: 12 additions & 0 deletions docs/commands/workflow_convert.rst
View file
Expand Up @@ -140,6 +140,12 @@ Convert Format 2 workflow to a native Galaxy workflow.
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file PATH Location of pid file is executed with
--daemon.
Expand All @@ -148,5 +154,11 @@ Convert Format 2 workflow to a native Galaxy workflow.
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.

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