-
Servers Offering this Tool
+Metadata
+Servers Offering this Tool
UseGalaxy.eu ({{ page.observed_tool_ids[0][1] }})This is a guess, we are not currently checking if that is actually present.
-Observed Tool Versions
+ +Observed Tool Versions
+Within GTN tutorials
+-
{% for tool in page.observed_tool_ids %}
- {{ tool[1] }} {% endfor %}
EDAM Operations
+-
+ {% for topic in site.data['tool-meta'][tool_id_path].edam_operations %}
+
- + + {{ topic }} + + + {% endfor %} +
EDAM Topics
+-
+ {% for topic in site.data['tool-meta'][tool_id_path].edam_topics %}
+
- + + {{ topic }} + + + {% endfor %} +
+
Relevant Tutorials
-
{% for tutorial in page.tutorial_list %}
-
diff --git a/_layouts/workflow.html b/_layouts/workflow.html
index 11ead822106762..dce3e843eab3fa 100644
--- a/_layouts/workflow.html
+++ b/_layouts/workflow.html
@@ -116,8 +116,9 @@
{{ workflow.title }}
{% if jekyll.environment == "production" %} -
Download Workflow RO-Crate
+ Download Workflow RO-Crate
{% endif %}
+
{% if workflow.workflowhub_id %}
View on WorkflowHub
{% endif %}
@@ -148,6 +149,70 @@ {{ workflow.title }}
Download{{ workflow.mermaid }}+Inputs
++ +
+ ++ + + + {% for input in workflow.inputs %} +Input +Label ++ + {% endfor %} + +{{ input.name }} +{{ input.label }} +Outputs
++ +
+ + ++ + + + {% for output in workflow.outputs %} +From +Output +Label ++ + {% endfor %} + +{{ output.tool_id }} +{{ output.name }} +{{ output.label }} +Tools
++ +
++ + + + {% for tool in workflow.workflow_tools %} +Tool +Links ++ + {% endfor %} + +{{ tool }} ++ {% if site.data['toolshed-revisions'][tool] %} + {% assign tsdata = site.data['toolshed-revisions'][tool] %} + + View in ToolShed + + {% endif %} + +To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.
diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index 8d38bb8769e7ae..0f6fd4b7475d8c 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -79,9 +79,9 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base } mat_contribs = [ + ['Workflow Author(s)', workflow['creators'].map { |c| c['name'] }], ['Tutorial Author(s)', Gtn::Contributors.get_authors(associated_material).map { |n| name2md(site, n) }], ['Tutorial Contributor(s)', Gtn::Contributors.get_non_authors(associated_material).map { |n| name2md(site, n) }], - ['Workflow Author(s)', workflow['creators'].map { |c| c['name'] }], ['Funder(s)', Gtn::Contributors.get_funders(associated_material).map { |n| name2md(site, n) }], ].reject { |_, v| v.empty? } @@ -90,7 +90,7 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base ## Associated Tutorial -This workflows is part of the tutorial [#{workflow['name']}](#{url}#{baseurl}/topics/#{workflow['topic_id']}/tutorials/#{workflow['tutorial_id']}/tutorial.html), available in the [GTN](https://training.galaxyproject.org) +This workflows is part of the tutorial [#{associated_material['title']}](#{url}#{baseurl}/topics/#{workflow['topic_id']}/tutorials/#{workflow['tutorial_id']}/tutorial.html), available in the [GTN](https://training.galaxyproject.org) #{"## Features" if features.values.any?} @@ -100,9 +100,8 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base #{mat_contribs.map { |k, v| "**#{k}**: #{v.join(', ')}" }.join("\n\n")} -[](https://training.galaxyproject.org/training-material/) +[](https://training.galaxyproject.org/training-material/) ).strip - #  crate = { '@context' => ['https://w3id.org/ro/crate/1.1/context'], diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index d6cc1e0bf368b7..c5b502d6c42ea3 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -699,7 +699,9 @@ def self.resolve_material(site, material) 'modified' => File.mtime(wf_path), 'mermaid' => mermaid(wf_json), 'graph_dot' => graph_dot(wf_json), - 'workflow_tools' => extract_workflow_tool_list(wf_json).uniq, + 'workflow_tools' => extract_workflow_tool_list(wf_json).flatten.uniq.sort, + 'inputs' => wf_json['steps'].select { |_k, v| ['data_input', 'data_collection_input', 'parameter_input'].include? v['type'] }.map{|_, v| v}, + 'outputs' => wf_json['steps'].select { |_k, v| v['workflow_outputs'] && v['workflow_outputs'].length.positive? }.map{|_, v| v}, } end end diff --git a/assets/images/ro-crate.png b/assets/images/ro-crate.png new file mode 100644 index 00000000000000..64b00a9a09df11 Binary files /dev/null and b/assets/images/ro-crate.png differ diff --git a/assets/images/workflowhub-icon.svg b/assets/images/workflowhub-icon.svg index 1c90ac0872b2f9..fc95a3e705a40f 100644 --- a/assets/images/workflowhub-icon.svg +++ b/assets/images/workflowhub-icon.svg @@ -2,23 +2,23 @@