--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/gxformat2/cytoscape.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,92 @@
+"""Build standalone visualization for Galaxy workflows."""
+import json
+import os
+import string
+import sys
+
+import pkg_resources
+
+from gxformat2._scripts import ensure_format2
+from gxformat2._yaml import ordered_load
+from gxformat2.converter import convert_inputs_to_steps, ensure_step_position, steps_as_list
+
+CYTOSCAPE_JS_TEMPLATE = pkg_resources.resource_filename(__name__, 'cytoscape.html')
+MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/"
+
+
+def main(argv=None):
+    """Entry point for building Cytoscape visualizations of Galaxy workflows."""
+    if argv is None:
+        argv = sys.argv[1:]
+
+    workflow_path = argv[0]
+    with open(workflow_path, "r") as f:
+        workflow_dict = ordered_load(f)
+
+    workflow_dict = ensure_format2(workflow_dict)
+    elements = []
+
+    steps = steps_as_list(workflow_dict)
+    convert_inputs_to_steps(workflow_dict, steps)
+
+    for i, step in enumerate(steps):
+        step_id = step.get("id") or step.get("label") or str(i)
+        step_type = step.get("type") or 'tool'
+        classes = ["type_%s" % step_type]
+        if step_type in ['tool', 'subworkflow']:
+            classes.append("runnable")
+        else:
+            classes.append("input")
+
+        tool_id = step.get("tool_id")
+        if tool_id and tool_id.startswith(MAIN_TS_PREFIX):
+            tool_id = tool_id[len(MAIN_TS_PREFIX):]
+        label = step.get("id") or step.get("label") or ("tool:%s" % tool_id) or str(i)
+        ensure_step_position(step, i)
+        node_position = dict(x=int(step["position"]["left"]), y=int(step["position"]["top"]))
+        repo_link = None
+        if "tool_shed_repository" in step:
+            repo = step["tool_shed_repository"]
+            repo_link = "https://" + repo["tool_shed"] + "/view/" + repo["owner"] + "/" + repo["name"] + "/" + repo["changeset_revision"]
+        node_data = {
+            "id": step_id,
+            "label": label,
+            "doc": step.get("doc"),
+            "tool_id": step.get("tool_id"),
+            "step_type": step_type,
+            "repo_link": repo_link
+        }
+        elements.append({"group": "nodes", "data": node_data, "classes": classes, "position": node_position})
+        for key, value in (step.get("in") or {}).items():
+            # handle lists?
+            if isinstance(value, dict) and 'source' in value:
+                value = value["source"]
+            elif isinstance(value, dict):
+                continue
+            if "/" in value:
+                from_step, output = value.split("/", 1)
+            else:
+                from_step, output = value, None
+            edge_id = "%s__to__%s" % (step_id, from_step)
+            edge_data = {"id": edge_id, "source": from_step, "target": step_id, "input": key, "output": output}
+            elements.append({"group": "edges", "data": edge_data})
+
+    if len(argv) > 1:
+        output_path = argv[1]
+    else:
+        output_path, _ = os.path.splitext(workflow_path)
+        output_path += ".html"
+
+    if output_path.endswith(".html"):
+        with open(CYTOSCAPE_JS_TEMPLATE, "r") as f:
+            template = f.read()
+        viz = string.Template(template).safe_substitute(elements=json.dumps(elements))
+        with open(output_path, "w") as f:
+            f.write(viz)
+    else:
+        with open(output_path, "w") as f:
+            json.dump(elements, f)
+
+
+if __name__ == "__main__":
+    main()