From 5d8db9c5e79d8c902b0aade4d7090a4498753a60 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 11 Mar 2024 12:00:06 +0100
Subject: [PATCH] update parameters
---
bioflow_insight_cli/main.py | 39 ++++++++++++++++++++++++++++++-------
1 file changed, 32 insertions(+), 7 deletions(-)
diff --git a/bioflow_insight_cli/main.py b/bioflow_insight_cli/main.py
index f622c79..31fdc4f 100644
--- a/bioflow_insight_cli/main.py
+++ b/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)
--
GitLab