diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py index c019b219bb45151beb975091a2b6be0aaddb43af..400bdd93026cf788486a61ea623e2171698e42e0 100644 --- a/run_workflow_phaeoexplorer.py +++ b/run_workflow_phaeoexplorer.py @@ -483,8 +483,8 @@ class RunWorkflow(speciesData.SpeciesData): # In case of the Jbrowse workflow, we unfortunately have to manually edit the parameters instead of setting them # as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error) if workflow_name == "Jbrowse": - workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "https://{host}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(host=self.config["host"], port=self.config["https_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")) - workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.abbreviation) + workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "https://{host}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(host=self.config["host"], port=self.config["https_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")) + workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.abbreviation) # Import the workflow in galaxy as a dict self.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)