update parameters

bioflow_insight_cli/main.py

@@ -7,26 +7,51 @@ from src.workflow import Workflow
 @click.command()
 @click.version_option(bioflow_insight_src.__version__)
 @click.argument('main_workflow_path')
-#@click.option('--author', 'author', required=False, help='Author name, extracted otherwise')
-@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo)')
-@click.option('--output-dir', default='./results', help='Where the results will be written')
+@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo).')
+@click.option('--date-published', 'datePublished', required=False, help='Publication date ("yyyy-mm-dd"), extracted otherwise (in the case of a Git repo).')
+@click.option('--description', 'description', required=False, help='Description of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--license', 'license', required=False, help='License of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--creative-work-status', 'creativeWorkStatus', required=False, help='Creative work status of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--version', 'version', required=False, help='Version of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--keywords', 'keywords', required=False, help='Keywords of workflow (fomat "keyword1, keyword2, ..."), extracted otherwise (in the case of a Git repo).')
+@click.option('--producer', 'producer', required=False, help='Producer of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--publisher', 'publisher', required=False, help='Publisher of workflow, extracted otherwise (in the case of a Git repo).')
 @click.option(
-    '--no-duplicate',
+    '--authors',
+    'authors',
+    required=False,
+    help=''
+    'Authors of workflow (format "[{\'@id\': "Author1", \'email\': "author1@email.com"}, ...]"), '
+    'extracted otherwise (in the case of a Git repo).',
+)
+
+@click.option('--output-dir', default='./results', help='Where the results will be written.')
+@click.option(
+    '--duplicate',
     'duplicate',
     required=False,
-    default=True,
+    default=False,
     is_flag=True,
     help=''
     'When processes and subworkflows are duplicated in the workflows by the \'include as\' option, '
     'this option will duplicate the procedures in the graph output.',
 )
 @click.option(
-    '--graph-in-dot-only',
+    '--render-graphs',
     'render_graphs',
     required=False,
     default=True,
     is_flag=True,
-    help='Generate the graph output only in dot format, not png (faster).',
+    help='Generate the graphs output in png format using graphviz (slower),'
+    'the mermaid and dot formats are always generated.',
+)
+@click.option(
+    '--display-info',
+    'display_info',
+    required=False,
+    default=True,
+    is_flag=True,
+    help='Option to show a visual summary of the analysis.',
 )
 def cli_command(main_workflow_path, **kwargs):
     return cli(main_workflow_path, **kwargs)