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comparison env/lib/python3.7/site-packages/planemo/options.py @ 5:9b1c78e6ba9c draft default tip

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 """Click definitions for various shared options and arguments."""
2
3 from __future__ import absolute_import
4
5 import functools
6 import os
7
8 import click
9 from galaxy.tool_util.deps import docker_util
10
11 from .config import planemo_option
12
13
14 def force_option(what="files"):
15 return planemo_option(
16 "-f",
17 "--force",
18 is_flag=True,
19 help="Overwrite existing %s if present." % what,
20 )
21
22
23 def skip_venv_option():
24 return planemo_option(
25 "--skip_venv",
26 is_flag=True,
27 help=("Do not create or source a virtualenv environment for Galaxy, "
28 "this should be used or instance to preserve an externally "
29 "configured virtual environment or conda environment.")
30 )
31
32
33 def run_engine_option():
34 return planemo_option(
35 "--engine",
36 type=click.Choice(["galaxy", "docker_galaxy", "cwltool", "toil", "external_galaxy"]),
37 default=None,
38 use_global_config=True,
39 help=("Select an engine to run or test artifacts such as tools "
40 "and workflows. Defaults to a local Galaxy, but running Galaxy within "
41 "a Docker container or the CWL reference implementation 'cwltool' and "
42 "'toil' be selected.")
43 )
44
45
46 def non_strict_cwl_option():
47 return planemo_option(
48 "--non_strict_cwl",
49 default=False,
50 is_flag=True,
51 help="Disable strict validation of CWL.",
52 )
53
54
55 def serve_engine_option():
56 return planemo_option(
57 "--engine",
58 type=click.Choice(["galaxy", "docker_galaxy", "external_galaxy"]),
59 default="galaxy",
60 use_global_config=True,
61 use_env_var=True,
62 help=("Select an engine to serve artifacts such as tools "
63 "and workflows. Defaults to a local Galaxy, but running Galaxy within "
64 "a Docker container.")
65 )
66
67
68 def ignore_dependency_problems_option():
69 return planemo_option(
70 "--ignore_dependency_problems",
71 is_flag=True,
72 default=False,
73 use_global_config=True,
74 help=("When installing shed repositories for workflows, ignore dependency issues. "
75 "These likely indicate a problem but in some cases may not prevent a workflow "
76 "from successfully executing.")
77 )
78
79
80 def cwltool_no_container_option():
81 return planemo_option(
82 "--no-container",
83 "--no_container",
84 is_flag=True,
85 default=False,
86 use_global_config=True,
87 help=("If cwltool engine is used, disable Docker container usage.")
88 )
89
90
91 def test_data_option():
92 return planemo_option(
93 "--test_data",
94 type=click.Path(exists=True, file_okay=False, resolve_path=True),
95 help="test-data directory to for specified tool(s).",
96 )
97
98
99 def extra_tools_option():
100 return planemo_option(
101 "--extra_tools",
102 type=click.Path(exists=True,
103 file_okay=True,
104 dir_okay=True,
105 resolve_path=True),
106 multiple=True,
107 help=("Extra tool sources to include in Galaxy's tool panel (file or "
108 "directory). These will not be linted/tested/etc... but they "
109 "will be available to workflows and for interactive use.")
110 )
111
112
113 def tool_data_table_option():
114 return planemo_option(
115 "--tool_data_table",
116 type=click.Path(exists=True, file_okay=True, resolve_path=True),
117 help="tool_data_table_conf.xml file to for specified tool(s).",
118 )
119
120
121 def galaxy_email_option():
122 return planemo_option(
123 "--galaxy_email",
124 type=str,
125 default="planemo@galaxyproject.org",
126 use_global_config=True,
127 use_env_var=True,
128 help="E-mail address to use when launching single-user Galaxy server.",
129 )
130
131
132 def galaxy_python_version():
133 return planemo_option(
134 '--galaxy_python_version',
135 use_global_config=True,
136 default=None,
137 type=click.Choice(['2', '2.7', '3', '3.5', '3.6', '3.7', '3.8']),
138 help="Python version to start Galaxy under",
139 )
140
141
142 def galaxy_root_option():
143 return planemo_option(
144 "--galaxy_root",
145 use_global_config=True,
146 extra_global_config_vars=["galaxy_root"],
147 use_env_var=True,
148 type=click.Path(file_okay=False, dir_okay=True, resolve_path=True),
149 help="Root of development galaxy directory to execute command with.",
150 )
151
152
153 def galaxy_cwl_root_option():
154 return planemo_option(
155 "--cwl_galaxy_root",
156 use_global_config=True,
157 extra_global_config_vars=["cwl_galaxy_root"],
158 use_env_var=True,
159 type=click.Path(exists=True, file_okay=False, resolve_path=True),
160 help=("Root of development galaxy directory to execute command with"
161 " (must be branch of Galaxy with CWL support, this option"
162 " is experimental and will be replaced with --galaxy_root when"
163 " and if CWL support is merged into Galaxy."),
164 )
165
166
167 def galaxy_port_option():
168 return planemo_option(
169 "--port",
170 type=int,
171 default="9090",
172 use_global_config=True,
173 help="Port to serve Galaxy on (default is 9090).",
174 )
175
176
177 def galaxy_host_option():
178 return planemo_option(
179 "--host",
180 type=str,
181 default="127.0.0.1",
182 use_global_config=True,
183 help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
184 "restricted to localhost connections for security reasons "
185 "set to 0.0.0.0 to bind Galaxy to all ports including "
186 "potentially publicly accessible ones."),
187 )
188
189
190 def dependency_resolvers_option():
191 return planemo_option(
192 "--dependency_resolvers_config_file",
193 type=click.Path(
194 exists=True,
195 file_okay=True,
196 dir_okay=False,
197 resolve_path=True
198 ),
199 use_global_config=True,
200 help="Dependency resolver configuration for Galaxy to target.",
201 )
202
203
204 def enable_cwl_option():
205 return planemo_option(
206 "--cwl",
207 is_flag=True,
208 help=("Configure Galaxy for use with CWL tool."
209 " (this option is experimental and will be replaced when"
210 " and if CWL support is merged into Galaxy)."),
211 )
212
213
214 def build_cwl_option():
215 return planemo_option(
216 "--cwl",
217 is_flag=True,
218 help="Build a CWL tool instead of a Galaxy tool.",
219 )
220
221
222 def run_output_directory_option():
223 return planemo_option(
224 "output_directory",
225 "--output_directory",
226 "--outdir",
227 type=click.Path(
228 file_okay=False,
229 dir_okay=True,
230 resolve_path=True,
231 ),
232 default=None,
233 help=("Where to store outputs of a 'run' task."),
234 )
235
236
237 def run_output_json_option():
238 return planemo_option(
239 "output_json",
240 "--output_json",
241 type=click.Path(
242 file_okay=True,
243 dir_okay=False,
244 resolve_path=True,
245 ),
246 default=None,
247 help=("Where to store JSON dictionary describing outputs of "
248 "a 'run' task."),
249 )
250
251
252 def no_dependency_resolution():
253 return planemo_option(
254 "--no_dependency_resolution",
255 is_flag=True,
256 help="Configure Galaxy with no dependency resolvers.",
257 )
258
259
260 def brew_dependency_resolution():
261 return planemo_option(
262 "--brew_dependency_resolution",
263 is_flag=True,
264 help="Configure Galaxy to use plain brew dependency resolution.",
265 )
266
267
268 def conda_dependency_resolution():
269 return planemo_option(
270 "--conda_dependency_resolution",
271 is_flag=True,
272 help="Configure Galaxy to use only conda for dependency resolution.",
273 )
274
275
276 def shed_dependency_resolution():
277 return planemo_option(
278 "--shed_dependency_resolution",
279 is_flag=True,
280 help=("Configure Galaxy to use brewed Tool Shed dependency"
281 " resolution."),
282 )
283
284
285 def file_path_option():
286 return planemo_option(
287 "--file_path",
288 type=click.Path(
289 file_okay=False,
290 dir_okay=True,
291 resolve_path=True
292 ),
293 help="Location for files created by Galaxy (e.g. database/files).",
294 default=None,
295 use_global_config=True,
296 )
297
298
299 def database_connection_option():
300 return planemo_option(
301 "--database_connection",
302 type=str,
303 help="Database connection string to use for Galaxy.",
304 default=None,
305 use_global_config=True,
306 )
307
308
309 def shed_tools_conf_option():
310 return planemo_option(
311 "--shed_tool_conf",
312 type=str,
313 help="Location of shed tools conf file for Galaxy.",
314 default=None,
315 use_global_config=True,
316 )
317
318
319 def shed_tools_directory_option():
320 return planemo_option(
321 "--shed_tool_path",
322 type=str,
323 help="Location of shed tools directory for Galaxy.",
324 default=None,
325 use_global_config=True,
326 )
327
328
329 def tool_dependency_dir_option():
330 return planemo_option(
331 "--tool_dependency_dir",
332 type=click.Path(
333 exists=True,
334 file_okay=False,
335 dir_okay=True,
336 resolve_path=True
337 ),
338 default=None,
339 use_global_config=True,
340 help="Tool dependency dir for Galaxy to target.",
341 )
342
343
344 def job_config_option():
345 return planemo_option(
346 "--job_config_file",
347 type=click.Path(
348 exists=True,
349 file_okay=True,
350 dir_okay=False,
351 resolve_path=True
352 ),
353 help="Job configuration file for Galaxy to target.",
354 default=None,
355 use_global_config=True,
356 )
357
358
359 def mulled_containers_option():
360 return planemo_option(
361 "mulled_containers",
362 "--mulled_containers",
363 "--biocontainers",
364 is_flag=True,
365 help="Test tools against mulled containers (forces --docker).",
366 )
367
368
369 def install_galaxy_option():
370 return planemo_option(
371 "--install_galaxy",
372 is_flag=True,
373 help="Download and configure a disposable copy of Galaxy from github."
374 )
375
376
377 def docker_galaxy_image_option():
378 return planemo_option(
379 "--docker_galaxy_image",
380 default="quay.io/bgruening/galaxy",
381 use_global_config=True,
382 help=("Docker image identifier for docker-galaxy-flavor used if "
383 "engine type is specified as ``docker-galaxy``. Defaults to "
384 "quay.io/bgruening/galaxy.")
385 )
386
387
388 def docker_extra_volume_option():
389 arg_type = click.Path(
390 exists=True,
391 file_okay=True,
392 dir_okay=True,
393 readable=True,
394 resolve_path=True,
395 )
396 return planemo_option(
397 "--docker_extra_volume",
398 type=arg_type,
399 default=None,
400 use_global_config=True,
401 help=("Extra path to mount if --engine docker.")
402 )
403
404
405 def galaxy_url_option():
406 return planemo_option(
407 "--galaxy_url",
408 use_global_config=True,
409 extra_global_config_vars=["galaxy_url"],
410 use_env_var=True,
411 type=str,
412 help="Remote Galaxy URL to use with external Galaxy engine.",
413 )
414
415
416 def galaxy_admin_key_option():
417 return planemo_option(
418 "--galaxy_admin_key",
419 use_global_config=True,
420 extra_global_config_vars=["admin_key"],
421 use_env_var=True,
422 type=str,
423 help="Admin key to use with external Galaxy engine.",
424 )
425
426
427 def galaxy_user_key_option():
428 return planemo_option(
429 "--galaxy_user_key",
430 use_global_config=True,
431 extra_global_config_vars=["admin_key"],
432 use_env_var=True,
433 type=str,
434 help="User key to use with external Galaxy engine.",
435 )
436
437
438 def no_cache_galaxy_option():
439 return planemo_option(
440 "--no_cache_galaxy",
441 is_flag=True,
442 help=("Skip caching of Galaxy source and dependencies obtained with "
443 "--install_galaxy. Not caching this results in faster "
444 "downloads (no git) - so is better on throw away instances such "
445 "with TravisCI. ")
446 )
447
448
449 def galaxy_branch_option():
450 return planemo_option(
451 "--galaxy_branch",
452 default=None,
453 use_global_config=True,
454 use_env_var=True,
455 help=("Branch of Galaxy to target (defaults to master) if a Galaxy "
456 "root isn't specified.")
457 )
458
459
460 def galaxy_source_option():
461 return planemo_option(
462 "--galaxy_source",
463 default=None,
464 use_global_config=True,
465 help=("Git source of Galaxy to target (defaults to the official "
466 "galaxyproject github source if a Galaxy root isn't "
467 "specified.")
468 )
469
470
471 def skip_install_option():
472 return planemo_option(
473 "--skip_install",
474 is_flag=True,
475 help="Skip installation - only source requirements already available."
476 )
477
478
479 def brew_option():
480 return planemo_option(
481 "--brew",
482 use_global_config=True,
483 type=click.Path(exists=True, file_okay=True, dir_okay=False),
484 help="Homebrew 'brew' executable to use."
485 )
486
487
488 def conda_prefix_option():
489 return planemo_option(
490 "--conda_prefix",
491 use_global_config=True,
492 use_env_var=True,
493 type=click.Path(file_okay=False, dir_okay=True),
494 help="Conda prefix to use for conda dependency commands."
495 )
496
497
498 def conda_exec_option():
499 return planemo_option(
500 "--conda_exec",
501 use_global_config=True,
502 type=click.Path(exists=True, file_okay=True, dir_okay=False),
503 help="Location of conda executable."
504 )
505
506
507 def conda_debug_option():
508 return planemo_option(
509 "--conda_debug",
510 is_flag=True,
511 help="Enable more verbose conda logging."
512 )
513
514
515 def conda_use_local_option():
516 return planemo_option(
517 "--conda_use_local",
518 is_flag=True,
519 help="Use locally built packages while building Conda environments."
520 )
521
522
523 def conda_ensure_channels_option():
524 return planemo_option(
525 "conda_ensure_channels",
526 "--conda_channels",
527 "--conda_ensure_channels",
528 type=str,
529 use_global_config=True,
530 use_env_var=True,
531 help=("Ensure conda is configured with specified comma separated "
532 "list of channels."),
533 default="iuc,conda-forge,bioconda,defaults",
534 )
535
536
537 def conda_copy_dependencies_option():
538 return planemo_option(
539 "--conda_copy_dependencies",
540 is_flag=True,
541 help=("Conda dependency resolution for Galaxy will copy dependencies "
542 "instead of attempting to link them.")
543 )
544
545
546 def conda_auto_install_option():
547 return planemo_option(
548 "--conda_auto_install/--no_conda_auto_install",
549 is_flag=True,
550 default=True,
551 help=("Conda dependency resolution for Galaxy will attempt to install "
552 "requested but missing packages.")
553 )
554
555
556 def conda_auto_init_option():
557 return planemo_option(
558 "--conda_auto_init/--no_conda_auto_init",
559 is_flag=True,
560 default=True,
561 help=("Conda dependency resolution for Galaxy will auto install "
562 "conda itself using miniconda if not availabe on conda_prefix.")
563 )
564
565
566 def conda_global_option():
567 return planemo_option(
568 "--global",
569 is_flag=True,
570 default=False,
571 help=("Install Conda dependencies globally instead of in requirement specific "
572 "environments packaged for tools. If the Conda bin directory is on your "
573 "PATH, tools may still use binaries but this is more designed for "
574 "interactive testing and debugging.")
575 )
576
577
578 def required_tool_arg(allow_uris=False):
579 """ Decorate click method as requiring the path to a single tool.
580 """
581 arg_type_class = click.Path if not allow_uris else UriLike
582 arg_type = arg_type_class(
583 exists=True,
584 file_okay=True,
585 dir_okay=False,
586 readable=True,
587 resolve_path=True,
588 )
589 if allow_uris:
590 name = "uri"
591 metavar = "TOOL_URI"
592 else:
593 name = "path"
594 metavar = "TOOL_PATH"
595 return click.argument(name, metavar=metavar, type=arg_type)
596
597
598 def paste_test_data_paths_option():
599 return planemo_option(
600 "--paste_test_data_paths/--no_paste_test_data_paths",
601 is_flag=True,
602 default=None,
603 help=("By default Planemo will use or not use Galaxy's path paste option to load "
604 "test data into a history based on the engine type it is targeting. This can "
605 "override the logic to explicitly enable or disable path pasting.")
606 )
607
608
609 def shed_install_option():
610 return planemo_option(
611 "--shed_install/--no_shed_install",
612 is_flag=True,
613 default=True,
614 help=("By default Planemo will attempt to install repositories needed for workflow "
615 "testing. This may not be appropriate for production servers and so this can "
616 "disabled by calling planemo with --no_shed_install.")
617 )
618
619
620 def single_user_mode_option():
621 return planemo_option(
622 "galaxy_single_user",
623 "--galaxy_single_user/--no_galaxy_single_user",
624 is_flag=True,
625 default=True,
626 help=("By default Planemo will configure Galaxy to run in single-user mode where there "
627 "is just one user and this user is automatically logged it. Use --no_galaxy_single_user "
628 "to prevent Galaxy from running this way.")
629 )
630
631
632 def required_workflow_arg():
633 arg_type = click.Path(
634 exists=True,
635 file_okay=True,
636 dir_okay=False,
637 readable=True,
638 resolve_path=False,
639 )
640 return click.argument("workflow_path", metavar="WORKFLOW_PATH", type=arg_type)
641
642
643 def required_job_arg():
644 """Decorate click method as requiring the path to a single tool.
645 """
646 arg_type = click.Path(
647 exists=True,
648 file_okay=True,
649 dir_okay=False,
650 readable=True,
651 resolve_path=False,
652 )
653 return click.argument("job_path", metavar="JOB_PATH", type=arg_type)
654
655
656 def _optional_tools_default(ctx, param, value):
657 if param.name in ["paths", "uris"] and len(value) == 0:
658 return [os.path.abspath(os.getcwd())]
659 else:
660 return value
661
662
663 def optional_tools_or_packages_arg(multiple=False):
664 """ Decorate click method as optionally taking in the path to a tool
665 or directory of tools or a Conda package. If no such argument is given
666 the current working directory will be treated as a directory of tools.
667 """
668 name = "paths" if multiple else "path"
669 nargs = -1 if multiple else 1
670 return click.argument(
671 name,
672 metavar="TARGET",
673 nargs=nargs,
674 )
675
676
677 class UriLike(click.Path):
678
679 def convert(self, value, param, ctx):
680 if "://" in value:
681 return value
682 else:
683 return super(UriLike, self).convert(value, param, ctx)
684
685
686 def optional_tools_arg(multiple=False, allow_uris=False):
687 """ Decorate click method as optionally taking in the path to a tool
688 or directory of tools. If no such argument is given the current working
689 directory will be treated as a directory of tools.
690 """
691 arg_type_class = click.Path if not allow_uris else UriLike
692 arg_type = arg_type_class(
693 exists=True,
694 file_okay=True,
695 dir_okay=True,
696 readable=True,
697 resolve_path=True,
698 )
699 if allow_uris:
700 name = "uris" if multiple else "uri"
701 else:
702 name = "paths" if multiple else "path"
703 nargs = -1 if multiple else 1
704 return click.argument(
705 name,
706 metavar="TOOL_PATH",
707 type=arg_type,
708 nargs=nargs,
709 callback=_optional_tools_default,
710 )
711
712
713 class ProjectOrRepositry(click.Path):
714
715 def __init__(self, **kwds):
716 super(ProjectOrRepositry, self).__init__(**kwds)
717
718 def convert(self, value, param, ctx):
719 if value and value.startswith("git:") or value.startswith("git+"):
720 return value
721 else:
722 return super(ProjectOrRepositry, self).convert(value, param, ctx)
723
724
725 def shed_project_arg(multiple=True):
726 arg_type = ProjectOrRepositry(
727 exists=True,
728 file_okay=False,
729 dir_okay=True,
730 resolve_path=True,
731 )
732 name = "paths" if multiple else "path"
733 nargs = -1 if multiple else 1
734 return click.argument(
735 name,
736 metavar="PROJECT",
737 type=arg_type,
738 nargs=nargs,
739 callback=_optional_tools_default,
740 )
741
742
743 def recipe_arg(multiple=True):
744 name = "paths" if multiple else "path"
745 nargs = -1 if multiple else 1
746 return click.argument(
747 name,
748 metavar="RECIPE_DIR",
749 type=click.Path(
750 exists=True,
751 file_okay=True,
752 dir_okay=True,
753 resolve_path=True,
754 ),
755 nargs=nargs,
756 callback=_optional_tools_default,
757 )
758
759
760 def optional_project_arg(exists=True, default="."):
761 arg_type = click.Path(
762 exists=exists,
763 file_okay=False,
764 dir_okay=True,
765 writable=True,
766 resolve_path=True,
767 )
768 return click.argument(
769 "path",
770 metavar="PROJECT",
771 default=default,
772 type=arg_type
773 )
774
775
776 def no_cleanup_option():
777 return planemo_option(
778 "--no_cleanup",
779 is_flag=True,
780 help=("Do not cleanup temp files created for and by Galaxy.")
781 )
782
783
784 def docker_enable_option():
785 return planemo_option(
786 "--docker/--no_docker",
787 default=False,
788 help=("Run Galaxy tools in Docker if enabled.")
789 )
790
791
792 def docker_cmd_option():
793 return planemo_option(
794 "--docker_cmd",
795 default=docker_util.DEFAULT_DOCKER_COMMAND,
796 help="Command used to launch docker (defaults to docker)."
797 )
798
799
800 def docker_sudo_option():
801 return planemo_option(
802 "--docker_sudo/--no_docker_sudo",
803 is_flag=True,
804 help="Flag to use sudo when running docker."
805 )
806
807
808 def docker_sudo_cmd_option():
809 return planemo_option(
810 "--docker_sudo_cmd",
811 help="sudo command to use when --docker_sudo is enabled " +
812 "(defaults to sudo).",
813 default=docker_util.DEFAULT_SUDO_COMMAND,
814 use_global_config=True,
815 )
816
817
818 def docker_host_option():
819 return planemo_option(
820 "--docker_host",
821 help="Docker host to target when executing docker commands " +
822 "(defaults to localhost).",
823 use_global_config=True,
824 default=docker_util.DEFAULT_HOST,
825 )
826
827
828 def docker_config_options():
829 return _compose(
830 docker_cmd_option(),
831 docker_sudo_option(),
832 docker_host_option(),
833 docker_sudo_cmd_option(),
834 )
835
836
837 def galaxy_docker_options():
838 return _compose(
839 docker_enable_option(),
840 docker_config_options(),
841 )
842
843
844 def shed_owner_option():
845 return planemo_option(
846 "--owner",
847 help="Tool Shed repository owner (username)."
848 )
849
850
851 def shed_name_option():
852 return planemo_option(
853 "--name",
854 help="Tool Shed repository name (defaults to the inferred "
855 "tool directory name)."
856 )
857
858
859 def validate_shed_target_callback(ctx, param, value):
860 if value is None:
861 ctx.fail("default_shed_target set to None, must specify a value for "
862 "--shed_target to run this command.")
863 return value
864
865
866 def shed_target_option():
867 return planemo_option(
868 "-t",
869 "--shed_target",
870 help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
871 "'local' (alias for http://localhost:9009/), an arbitrary url "
872 "or mappings defined ~/.planemo.yml.",
873 default=None,
874 use_global_config=True,
875 callback=validate_shed_target_callback,
876 )
877
878
879 def shed_key_option():
880 return planemo_option(
881 "--shed_key",
882 help=("API key for Tool Shed access. An API key is required unless "
883 "e-mail and password is specified. This key can be specified "
884 "with either --shed_key or --shed_key_from_env.")
885 )
886
887
888 def shed_key_from_env_option():
889 return planemo_option(
890 "--shed_key_from_env",
891 help="Environment variable to read API key for Tool Shed access from."
892 )
893
894
895 def shed_email_option():
896 return planemo_option(
897 "--shed_email",
898 help="E-mail for Tool Shed auth (required unless shed_key is "
899 "specified)."
900 )
901
902
903 def shed_password_option():
904 return planemo_option(
905 "--shed_password",
906 help="Password for Tool Shed auth (required unless shed_key is "
907 "specified)."
908 )
909
910
911 def shed_skip_upload():
912 return planemo_option(
913 "--skip_upload",
914 is_flag=True,
915 help=("Skip upload contents as part of operation, only update "
916 "metadata.")
917 )
918
919
920 def shed_skip_metadata():
921 return planemo_option(
922 "--skip_metadata",
923 is_flag=True,
924 help=("Skip metadata update as part of operation, only upload "
925 "new contents.")
926 )
927
928
929 def shed_message_option():
930 return planemo_option(
931 "-m",
932 "--message",
933 help="Commit message for tool shed upload."
934 )
935
936
937 def shed_force_create_option():
938 return planemo_option(
939 "--force_repository_creation",
940 help=("If a repository cannot be found for the specified user/repo "
941 "name pair, then automatically create the repository in the "
942 "toolshed."),
943 is_flag=True,
944 default=False
945 )
946
947
948 def shed_check_diff_option():
949 return planemo_option(
950 "--check_diff",
951 is_flag=True,
952 help=("Skip uploading if the shed_diff detects there would be no "
953 "'difference' (only attributes populated by the shed would "
954 "be updated.)")
955 )
956
957
958 def shed_upload_options():
959 return _compose(
960 shed_message_option(),
961 shed_force_create_option(),
962 shed_check_diff_option(),
963 )
964
965
966 def shed_realization_options():
967 return _compose(
968 shed_project_arg(multiple=True),
969 recursive_shed_option(),
970 shed_fail_fast_option(),
971 )
972
973
974 def shed_repo_options():
975 return _compose(
976 shed_owner_option(),
977 shed_name_option(),
978 )
979
980
981 def shed_publish_options():
982 """ Common options for commands that require publishing to a
983 a shed.
984 """
985 return _compose(
986 shed_realization_options(),
987 shed_repo_options(),
988 shed_target_options(),
989 )
990
991
992 def shed_read_options():
993 """ Common options that require read access to mapped repositories
994 in a shed.
995 """
996 return _compose(
997 shed_realization_options(),
998 shed_repo_options(),
999 shed_target_options(),
1000 )
1001
1002
1003 def shed_target_options():
1004 """ Common options for commands that require read-only
1005 interactions with a shed.
1006 """
1007 return _compose(
1008 shed_email_option(),
1009 shed_key_option(),
1010 shed_key_from_env_option(),
1011 shed_password_option(),
1012 shed_target_option(),
1013 )
1014
1015
1016 def conda_target_options(include_local=True):
1017 return _compose(
1018 conda_prefix_option(),
1019 conda_exec_option(),
1020 conda_debug_option(),
1021 conda_ensure_channels_option(),
1022 conda_use_local_option(),
1023 )
1024
1025
1026 def galaxy_run_options():
1027 return _compose(
1028 galaxy_target_options(),
1029 galaxy_port_option(),
1030 galaxy_host_option(),
1031 )
1032
1033
1034 def galaxy_config_options():
1035 return _compose(
1036 test_data_option(),
1037 tool_data_table_option(),
1038 dependency_resolvers_option(),
1039 brew_dependency_resolution(),
1040 shed_dependency_resolution(),
1041 no_dependency_resolution(),
1042 conda_target_options(),
1043 conda_dependency_resolution(),
1044 conda_copy_dependencies_option(),
1045 conda_auto_install_option(),
1046 conda_auto_init_option(),
1047 # Profile options...
1048 profile_option(),
1049 profile_database_options(),
1050 file_path_option(),
1051 database_connection_option(),
1052 shed_tools_conf_option(),
1053 shed_tools_directory_option(),
1054 single_user_mode_option(),
1055 )
1056
1057
1058 def galaxy_target_options():
1059 return _compose(
1060 galaxy_root_option(),
1061 galaxy_python_version(),
1062 extra_tools_option(),
1063 install_galaxy_option(),
1064 galaxy_branch_option(),
1065 galaxy_source_option(),
1066 skip_venv_option(),
1067 no_cache_galaxy_option(),
1068 no_cleanup_option(),
1069 galaxy_email_option(),
1070 galaxy_docker_options(),
1071 mulled_containers_option(),
1072 # Profile options...
1073 job_config_option(),
1074 tool_dependency_dir_option(),
1075 )
1076
1077
1078 def pid_file_option():
1079 pid_file_type = click.Path(
1080 file_okay=True,
1081 dir_okay=False,
1082 resolve_path=True,
1083 )
1084 return planemo_option(
1085 "--pid_file",
1086 type=pid_file_type,
1087 default=None,
1088 help="Location of pid file is executed with --daemon."
1089 )
1090
1091
1092 def daemon_option():
1093 return planemo_option(
1094 "--daemon",
1095 is_flag=True,
1096 help="Serve Galaxy process as a daemon."
1097 )
1098
1099
1100 def profile_option():
1101 return planemo_option(
1102 "--profile",
1103 type=str,
1104 default=None,
1105 help=("Name of profile (created with the profile_create command) to use "
1106 "with this command.")
1107 )
1108
1109
1110 def galaxy_serve_options():
1111 return _compose(
1112 galaxy_run_options(),
1113 serve_engine_option(),
1114 non_strict_cwl_option(),
1115 docker_galaxy_image_option(),
1116 docker_extra_volume_option(),
1117 galaxy_config_options(),
1118 daemon_option(),
1119 pid_file_option(),
1120 ignore_dependency_problems_option(),
1121 shed_install_option()
1122 )
1123
1124
1125 def training_topic_name_option():
1126 return planemo_option(
1127 "--topic_name",
1128 required=True,
1129 help="Name (directory name) of the topic to create or in which "
1130 "a tutorial should be created or updates"
1131 )
1132
1133
1134 def training_topic_option():
1135 return _compose(
1136 training_topic_name_option(),
1137 planemo_option(
1138 "--topic_title",
1139 default="Title of the topic",
1140 help="Title of the topic to create"),
1141 planemo_option(
1142 "--topic_summary",
1143 default="Summary of the topic",
1144 help="Summary of the topic"),
1145 planemo_option(
1146 "--topic_target",
1147 type=click.Choice(['use', 'admin-dev', 'instructors']),
1148 default="use",
1149 help="Target audience for the topic")
1150 )
1151
1152
1153 def training_tutorial_name_option():
1154 return planemo_option(
1155 "--tutorial_name",
1156 help="Name (directory name) of the tutorial to create or to modify"
1157 )
1158
1159
1160 def training_tutorial_name_req_option():
1161 return planemo_option(
1162 "--tutorial_name",
1163 required=True,
1164 help="Name (directory name) of the tutorial to modify"
1165 )
1166
1167
1168 def training_datatype_option():
1169 return planemo_option(
1170 "--datatypes",
1171 type=click.Path(file_okay=True, resolve_path=True),
1172 help="YAML file with the correspondance between Zenodo extension and Galaxy datatypes",
1173 default="shared/datatypes.yaml"
1174 )
1175
1176
1177 def training_zenodo_option():
1178 return planemo_option(
1179 "--zenodo_link",
1180 help="Zenodo URL with the input data")
1181
1182
1183 def training_tutorial_worflow_option():
1184 return _compose(
1185 planemo_option(
1186 "--workflow",
1187 type=click.Path(file_okay=True, resolve_path=True),
1188 help="Workflow of the tutorial (locally)",
1189 default=None),
1190 planemo_option(
1191 "--galaxy_url",
1192 help="URL of a Galaxy instance with the workflow"),
1193 planemo_option(
1194 "--galaxy_api_key",
1195 help="API key on the Galaxy instance with the workflow"),
1196 planemo_option(
1197 "--workflow_id",
1198 help="ID of the workflow on the Galaxy instance")
1199 )
1200
1201
1202 def training_tutorial_option():
1203 return _compose(
1204 training_tutorial_name_option(),
1205 planemo_option(
1206 "--tutorial_title",
1207 default="Title of the tutorial",
1208 help="Title of the tutorial"),
1209 planemo_option(
1210 "--hands_on",
1211 is_flag=True,
1212 default=True,
1213 help="Add hands-on for the new tutorial"),
1214 planemo_option(
1215 "--slides",
1216 is_flag=True,
1217 default=False,
1218 help="Add slides for the new tutorial"),
1219 training_tutorial_worflow_option(),
1220 training_zenodo_option()
1221 )
1222
1223
1224 def training_init_options():
1225 return _compose(
1226 training_topic_option(),
1227 training_tutorial_option(),
1228 training_datatype_option()
1229 )
1230
1231
1232 def training_fill_data_library_options():
1233 return _compose(
1234 training_topic_name_option(),
1235 training_tutorial_name_req_option(),
1236 training_zenodo_option(),
1237 training_datatype_option()
1238 )
1239
1240
1241 def training_generate_tuto_from_wf_options():
1242 return _compose(
1243 training_topic_name_option(),
1244 training_tutorial_name_req_option(),
1245 training_tutorial_worflow_option()
1246 )
1247
1248
1249 def shed_fail_fast_option():
1250 return planemo_option(
1251 "--fail_fast",
1252 is_flag=True,
1253 default=False,
1254 help="If multiple repositories are specified and an error occurs "
1255 "stop immediately instead of processing remaining repositories."
1256 )
1257
1258
1259 def lint_xsd_option():
1260 return planemo_option(
1261 "--xsd/--no_xsd",
1262 is_flag=True,
1263 default=True,
1264 help=("Include tool XSD validation in linting process.")
1265 )
1266
1267
1268 def report_level_option():
1269 return planemo_option(
1270 "--report_level",
1271 type=click.Choice(["all", "warn", "error"]),
1272 default="all",
1273 )
1274
1275
1276 def report_xunit():
1277 return planemo_option(
1278 "--report_xunit",
1279 type=click.Path(file_okay=True, resolve_path=True),
1280 help="Output an XUnit report, useful for CI testing",
1281 default=None,
1282 )
1283
1284
1285 def skip_option():
1286 return planemo_option(
1287 "-s",
1288 "--skip",
1289 default=None,
1290 help=("Comma-separated list of lint tests to skip (e.g. passing "
1291 "--skip 'citations,xml_order' would skip linting of citations "
1292 "and best-practice XML ordering.")
1293 )
1294
1295
1296 def fail_level_option():
1297 return planemo_option(
1298 "--fail_level",
1299 type=click.Choice(['warn', 'error']),
1300 default="warn"
1301 )
1302
1303
1304 def recursive_shed_option():
1305 return recursive_option(
1306 "Recursively perform command for nested repository directories.",
1307 )
1308
1309
1310 def recursive_option(help="Recursively perform command for subdirectories."):
1311 return planemo_option(
1312 "-r",
1313 "--recursive",
1314 is_flag=True,
1315 help=help,
1316 )
1317
1318
1319 def merge_test_json():
1320 target_path = click.Path(
1321 file_okay=True,
1322 dir_okay=False,
1323 resolve_path=True,
1324 )
1325 return click.argument(
1326 'input_paths',
1327 metavar="INPUT_PATHS",
1328 type=target_path,
1329 nargs=-1,
1330 )
1331
1332
1333 def tool_test_json(var="path"):
1334 target_path = click.Path(
1335 file_okay=True,
1336 dir_okay=False,
1337 resolve_path=True,
1338 )
1339 return click.argument(
1340 var,
1341 metavar="FILE_PATH",
1342 type=target_path,
1343 default="tool_test_output.json",
1344 )
1345
1346
1347 def engine_options():
1348 return _compose(
1349 run_engine_option(),
1350 non_strict_cwl_option(),
1351 cwltool_no_container_option(),
1352 docker_galaxy_image_option(),
1353 docker_extra_volume_option(),
1354 ignore_dependency_problems_option(),
1355 shed_install_option(),
1356 galaxy_url_option(),
1357 galaxy_admin_key_option(),
1358 galaxy_user_key_option(),
1359 )
1360
1361
1362 def test_report_options():
1363 return _compose(
1364 planemo_option(
1365 "--test_output",
1366 type=click.Path(file_okay=True, resolve_path=True),
1367 use_global_config=True,
1368 default="tool_test_output.html",
1369 help=("Output test report (HTML - for humans) defaults to "
1370 "tool_test_output.html."),
1371 ),
1372 planemo_option(
1373 "--test_output_text",
1374 type=click.Path(file_okay=True, resolve_path=True),
1375 use_global_config=True,
1376 help=("Output test report (Basic text - for display in CI)"),
1377 default=None,
1378 ),
1379 planemo_option(
1380 "--test_output_markdown",
1381 type=click.Path(file_okay=True, resolve_path=True),
1382 use_global_config=True,
1383 help=("Output test report (Markdown style - for humans & "
1384 "computers)"),
1385 default=None,
1386 ),
1387 planemo_option(
1388 "--test_output_xunit",
1389 type=click.Path(file_okay=True, resolve_path=True),
1390 use_global_config=True,
1391 help=("Output test report (xunit style - for CI systems"),
1392 default=None,
1393 ),
1394 planemo_option(
1395 "--test_output_junit",
1396 type=click.Path(file_okay=True, resolve_path=True),
1397 use_global_config=True,
1398 help=("Output test report (jUnit style - for CI systems"),
1399 default=None,
1400 ),
1401 )
1402
1403
1404 def profile_name_argument():
1405 return click.argument(
1406 'profile_name',
1407 metavar="PROFILE_NAME",
1408 type=str,
1409 )
1410
1411
1412 def database_identifier_argument():
1413 return click.argument(
1414 'identifier',
1415 metavar="IDENTIFIER",
1416 type=str,
1417 )
1418
1419
1420 def postgres_datatype_type_option():
1421 return planemo_option(
1422 "--postgres",
1423 "database_type",
1424 flag_value="postgres",
1425 help=("Use postgres database type."),
1426 )
1427
1428
1429 def database_type_option():
1430 return planemo_option(
1431 "--database_type",
1432 default="auto",
1433 type=click.Choice([
1434 "postgres",
1435 "postgres_docker",
1436 "sqlite",
1437 "auto",
1438 ]),
1439 use_global_config=True,
1440 help=("Type of database to use for profile - "
1441 "'auto', 'sqlite', 'postgres', and 'postgres_docker' are available options. "
1442 "Use postgres to use an existing postgres server you user can "
1443 "access without a password via the psql command. Use postgres_docker "
1444 "to have Planemo manage a docker container running postgres. "
1445 "Data with postgres_docker is not yet persisted past when you restart "
1446 "the docker container launched by Planemo so be careful with this option."),
1447 )
1448
1449
1450 def database_source_options():
1451 """Database connection options for commands that utilize a database."""
1452 return _compose(
1453 planemo_option(
1454 "--postgres_psql_path",
1455 default="psql",
1456 use_global_config=True,
1457 help=("Name or or path to postgres client binary (psql)."),
1458 ),
1459 planemo_option(
1460 "--postgres_database_user",
1461 default="postgres",
1462 use_global_config=True,
1463 help=("Postgres username for managed development databases."),
1464 ),
1465 planemo_option(
1466 "--postgres_database_host",
1467 default=None,
1468 use_global_config=True,
1469 help=("Postgres host name for managed development databases."),
1470 ),
1471 planemo_option(
1472 "--postgres_database_port",
1473 default=None,
1474 use_global_config=True,
1475 help=("Postgres port for managed development databases."),
1476 ),
1477 )
1478
1479
1480 def profile_database_options():
1481 return _compose(
1482 postgres_datatype_type_option(),
1483 database_type_option(),
1484 database_source_options(),
1485 )
1486
1487
1488 def test_options():
1489 return _compose(
1490 planemo_option(
1491 "--update_test_data",
1492 is_flag=True,
1493 help="Update test-data directory with job outputs (normally"
1494 " written to directory --job_output_files if specified.)"
1495 ),
1496 paste_test_data_paths_option(),
1497 test_report_options(),
1498 planemo_option(
1499 "--test_output_json",
1500 type=click.Path(file_okay=True, resolve_path=True),
1501 use_global_config=True,
1502 help=("Output test report (planemo json) defaults to "
1503 "tool_test_output.json."),
1504 default="tool_test_output.json",
1505 ),
1506 planemo_option(
1507 "--job_output_files",
1508 type=click.Path(file_okay=False, resolve_path=True),
1509 help="Write job outputs to specified directory.",
1510 default=None,
1511 ),
1512 planemo_option(
1513 "--summary",
1514 type=click.Choice(["none", "minimal", "compact"]),
1515 default="minimal",
1516 help=("Summary style printed to planemo's standard output (see "
1517 "output reports for more complete summary). Set to 'none' "
1518 "to disable completely.")
1519 )
1520 )
1521
1522
1523 def _compose(*functions):
1524 def compose2(f, g):
1525 return lambda x: f(g(x))
1526 return functools.reduce(compose2, functions)
1527
1528
1529 def dependencies_script_options():
1530 return _compose(
1531 planemo_option(
1532 "--download_cache",
1533 type=click.Path(file_okay=False, resolve_path=True),
1534 use_global_config=True,
1535 help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
1536 default=None,
1537 ),
1538 )
1539
1540
1541 def filter_exclude_option():
1542 return planemo_option(
1543 "--exclude",
1544 type=click.Path(resolve_path=False),
1545 multiple=True,
1546 help="Paths to exclude.",
1547 )
1548
1549
1550 def filter_exclude_from_option():
1551 return planemo_option(
1552 "--exclude_from",
1553 type=click.Path(exists=True, file_okay=True, dir_okay=False, resolve_path=True),
1554 multiple=True,
1555 help="File of paths to exclude.",
1556 )
1557
1558
1559 def filter_changed_in_commit_option():
1560 return planemo_option(
1561 "--changed_in_commit_range",
1562 help="Exclude paths unchanged in git commit range.",
1563 )
1564
1565
1566 def ci_chunk_count_option():
1567 return planemo_option(
1568 "--chunk_count",
1569 type=int,
1570 help="Split output into chunks of this many item and print --chunk such group.",
1571 default=1,
1572 )
1573
1574
1575 def ci_chunk_option():
1576 return planemo_option(
1577 "--chunk",
1578 type=int,
1579 help=("When output is split into --chunk_count groups, output the group 0-indexed"
1580 "by this option."),
1581 default=0,
1582 )
1583
1584
1585 def ci_output_option():
1586 return planemo_option(
1587 "--output",
1588 help="File to output to, or - for standard output.",
1589 default="-",
1590 )
1591
1592
1593 def ci_find_options():
1594 return _compose(
1595 filter_exclude_option(),
1596 filter_exclude_from_option(),
1597 filter_changed_in_commit_option(),
1598 ci_chunk_count_option(),
1599 ci_chunk_option(),
1600 ci_output_option(),
1601 )
1602
1603
1604 def tool_init_id_option(prompt=True):
1605 return planemo_option(
1606 "-i",
1607 "--id",
1608 type=click.STRING,
1609 prompt=prompt,
1610 help="Short identifier for new tool (no whitespace)",
1611 )
1612
1613
1614 def tool_init_tool_option():
1615 return planemo_option(
1616 "-t",
1617 "--tool",
1618 default=None,
1619 type=click.Path(exists=False,
1620 file_okay=True,
1621 dir_okay=False,
1622 writable=True,
1623 resolve_path=True),
1624 help="Output path for new tool (default is <id>.xml)",
1625 )
1626
1627
1628 def tool_init_name_option(prompt=True, help="Name for new tool (user facing)"):
1629 return planemo_option(
1630 "-n",
1631 "--name",
1632 type=click.STRING,
1633 prompt=prompt,
1634 help=help,
1635 )
1636
1637
1638 def tool_init_version_option():
1639 return planemo_option(
1640 "--version",
1641 default="0.1.0",
1642 type=click.STRING,
1643 help="Tool XML version.",
1644 )
1645
1646
1647 def tool_init_description_option():
1648 return planemo_option(
1649 "-d",
1650 "--description",
1651 type=click.STRING,
1652 default=None,
1653 prompt=False,
1654 help="Short description for new tool (user facing)",
1655 )
1656
1657
1658 def tool_init_command_option():
1659 return planemo_option(
1660 "-c",
1661 "--command",
1662 type=click.STRING,
1663 default=None,
1664 prompt=False,
1665 help=("Command potentially including cheetah variables ()"
1666 "(e.g. 'seqtk seq -a $input > $output')"),
1667 )
1668
1669
1670 def tool_init_doi_option():
1671 return planemo_option(
1672 "--doi",
1673 type=click.STRING,
1674 default=None,
1675 multiple=True,
1676 prompt=False,
1677 help=("Supply a DOI (http://www.doi.org/) easing citation of the tool "
1678 "for Galxy users (e.g. 10.1101/014043).")
1679 )
1680
1681
1682 def tool_init_test_case_option():
1683 return planemo_option(
1684 "--test_case",
1685 is_flag=True,
1686 default=None,
1687 prompt=False,
1688 help=("For use with --example_commmand, generate a tool test case from "
1689 "the supplied example."),
1690 )
1691
1692
1693 def tool_init_macros_option():
1694 return planemo_option(
1695 "--macros",
1696 is_flag=True,
1697 default=None,
1698 prompt=False,
1699 help="Generate a macros.xml for reuse across many tools.",
1700 )
1701
1702
1703 def tool_init_cite_url_option():
1704 return planemo_option(
1705 "--cite_url",
1706 type=click.STRING,
1707 default=None,
1708 multiple=True,
1709 prompt=False,
1710 help=("Supply a URL for citation.")
1711 )
1712
1713
1714 def tool_init_input_option():
1715 return planemo_option(
1716 "--input",
1717 type=click.STRING,
1718 default=None,
1719 prompt=False,
1720 multiple=True,
1721 help="An input description (e.g. input.fasta)",
1722 )
1723
1724
1725 def tool_init_output_option():
1726 return planemo_option(
1727 "--output",
1728 type=click.STRING,
1729 multiple=True,
1730 default=None,
1731 prompt=False,
1732 help=("An output location (e.g. output.bam), the Galaxy datatype is "
1733 "inferred from the extension."),
1734 )
1735
1736
1737 def tool_init_help_text_option():
1738 return planemo_option(
1739 "--help_text",
1740 type=click.STRING,
1741 default=None,
1742 prompt=False,
1743 help="Help text (reStructuredText)",
1744 )
1745
1746
1747 def tool_init_help_from_command_option():
1748 return planemo_option(
1749 "--help_from_command",
1750 type=click.STRING,
1751 default=None,
1752 prompt=False,
1753 help="Auto populate help from supplied command.",
1754 )
1755
1756
1757 def tool_init_example_input_option():
1758 return planemo_option(
1759 "--example_input",
1760 type=click.STRING,
1761 default=None,
1762 prompt=False,
1763 multiple=True,
1764 help=("For use with --example_command, replace input file (e.g. 2.fastq "
1765 "with a data input parameter)."),
1766 )
1767
1768
1769 def tool_init_example_output_option():
1770 return planemo_option(
1771 "--example_output",
1772 type=click.STRING,
1773 default=None,
1774 prompt=False,
1775 multiple=True,
1776 help=("For use with --example_command, replace input file (e.g. 2.fastq "
1777 "with a tool output)."),
1778 )
1779
1780
1781 def tool_init_named_output_option():
1782 return planemo_option(
1783 "--named_output",
1784 type=click.STRING,
1785 multiple=True,
1786 default=None,
1787 prompt=False,
1788 help=("Create a named output for use with command block for example "
1789 "specify --named_output=output1.bam and then use '-o $output1' "
1790 "in your command block."),
1791 )
1792
1793
1794 def tool_init_version_command_option():
1795 return planemo_option(
1796 "--version_command",
1797 type=click.STRING,
1798 default=None,
1799 prompt=False,
1800 help="Command to print version (e.g. 'seqtk --version')",
1801 )
1802
1803
1804 REQUIREMENT_HELP = "Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68')."
1805
1806
1807 def tool_init_requirement_option(help=REQUIREMENT_HELP):
1808 return planemo_option(
1809 "--requirement",
1810 type=click.STRING,
1811 default=None,
1812 multiple=True,
1813 prompt=False,
1814 help=help,
1815 )
1816
1817
1818 def tool_init_container_option():
1819 return planemo_option(
1820 "--container",
1821 type=click.STRING,
1822 default=None,
1823 multiple=True,
1824 prompt=False,
1825 help="Add a Docker image identifier for this tool."
1826 )
1827
1828
1829 EXAMPLE_COMMAND_HELP = (
1830 "Example to command with paths to build Cheetah template from "
1831 "(e.g. 'seqtk seq -a 2.fastq > 2.fasta'). Option cannot be used "
1832 "with --command, should be used --example_input and "
1833 "--example_output."
1834 )
1835
1836
1837 def tool_init_example_command_option(help=EXAMPLE_COMMAND_HELP):
1838 return planemo_option(
1839 "--example_command",
1840 type=click.STRING,
1841 default=None,
1842 prompt=False,
1843 help=help,
1844 )
1845
1846
1847 def mulled_conda_option():
1848 return planemo_option(
1849 "--mulled_conda_version",
1850 type=click.STRING,
1851 default=None,
1852 help=("Install a specific version of Conda before running the command, by "
1853 "default the version that comes with the continuumio miniconda3 image "
1854 "will be used under Linux and under Mac OS X Conda will be upgraded to "
1855 "to work around a bug in 4.2.")
1856 )
1857
1858
1859 def mulled_namespace_option():
1860 return planemo_option(
1861 "--mulled_namespace",
1862 type=click.STRING,
1863 default="biocontainers",
1864 help=("Build a mulled image with the specified namespace - defaults to "
1865 "biocontainers. Galaxy currently only recognizes images with the "
1866 "namespace biocontainers.")
1867 )
1868
1869
1870 def mulled_action_option():
1871 return planemo_option(
1872 "--mulled_command",
1873 type=click.STRING,
1874 default="build-and-test",
1875 help=("Mulled action to perform for targets - this defaults to 'build-and-test'.")
1876 )
1877
1878
1879 def mulled_options():
1880 return _compose(
1881 mulled_conda_option(),
1882 mulled_namespace_option(),
1883 mulled_action_option(),
1884 )