<commit_before>{
    "ver": "1.4.0",
    "authors": [
        "dylan"
    ],
    "contact": "http://kbase.us/contact-us/",
    "visible": true,
    "categories": ["active", "comparative_genomics"],
    "widgets": {
        "input": null,
        "output": "no-display"
    },
    "parameters": [ 
        {
            "id": "input_pangenome_ref",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "" ],
            "field_type": "text",
            "text_options": {
                "valid_ws_types": [ "KBaseGenomes.Pangenome" ]
            }
        },
        {
            "id": "input_speciesTree_ref",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "" ],
            "field_type": "text",
            "text_options": {
                "valid_ws_types": [ "KBaseTrees.Tree" ]
            }
        },
        {
            "id": "save_featuresets",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "0" ],
            "field_type": "dropdown",
            "dropdown_options": {
                "options": [
                                {
                                        "value": "0",
                                        "display": "DON'T save feature sets",
                                        "id": "save_featuresets-dont",
                                        "ui-name": "save_featuresets-dont"
                                },
                                {
                                        "value": "1",
                                        "display": "DO save feature sets",
                                        "id": "save_featuresets-do",
                                        "ui-name": "save_featuresets-do"
                                }
                ]
            }
        },
        {
            "id": "skip_missing_genomes",
            "optional": false,
            "advanced": true,
            "allow_multiple": false,
            "default_values": [ "0" ],
            "field_type": "dropdown",
            "dropdown_options": {
	    	"options": [
				{
					"value": "1",
					"display": "require all genomes be in Pangenome",
					"id": "show",
					"ui-name": "show"
				},
				{
					"value": "0",
					"display": "ignore genomes not in Pangenome",
					"id": "hide",
					"ui-name": "hide"
				}
		]
            }
        },
        {
            "id": "enforce_genome_version_match",
            "optional": false,
            "advanced": true,
            "allow_multiple": false,
            "default_values": [ "0" ],
            "field_type": "dropdown",
            "dropdown_options": {
	    	"options": [
				{
					"value": "1",
					"display": "require genome version match",
					"id": "show",
					"ui-name": "show"
				},
				{
					"value": "0",
					"display": "use newest genome version",
					"id": "hide",
					"ui-name": "hide"
				}
		]
            }
        }
    ],
    "behavior": {
        "service-mapping": {
            "url": "",
            "name": "kb_phylogenomics",
            "method": "view_pan_phylo",
            "input_mapping": [
                {
                    "narrative_system_variable": "workspace",
                    "target_property": "workspace_name"
                },
                {
                    "input_parameter": "input_pangenome_ref",
		    "target_property": "input_pangenome_ref",
		    "target_type_transform": "resolved-ref"
                },
                {
                    "input_parameter": "input_speciesTree_ref",
		    "target_property": "input_speciesTree_ref",
		    "target_type_transform": "resolved-ref"
                },
                {
                    "input_parameter": "save_featuresets",
		    "target_property": "save_featuresets"
                },
                {
                    "input_parameter": "skip_missing_genomes",
		    "target_property": "skip_missing_genomes"
                },
                {
                    "input_parameter": "enforce_genome_version_match",
		    "target_property": "enforce_genome_version_match"
                }
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            "output_mapping": [
                {
                    "service_method_output_path": [0, "report_name"],
                    "target_property": "report_name"
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                {
                    "service_method_output_path": [0, "report_ref"],
                    "target_property": "report_ref"
                },
                {
                    "narrative_system_variable": "workspace",
                    "target_property": "workspace_name"
                }
            ]
        }
    },
    "job_id_output_field": "docker"
}
<commit_msg>updated defaults for skip option<commit_after>{
    "ver": "1.4.0",
    "authors": [
        "dylan"
    ],
    "contact": "http://kbase.us/contact-us/",
    "visible": true,
    "categories": ["active", "comparative_genomics"],
    "widgets": {
        "input": null,
        "output": "no-display"
    },
    "parameters": [ 
        {
            "id": "input_pangenome_ref",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "" ],
            "field_type": "text",
            "text_options": {
                "valid_ws_types": [ "KBaseGenomes.Pangenome" ]
            }
        },
        {
            "id": "input_speciesTree_ref",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "" ],
            "field_type": "text",
            "text_options": {
                "valid_ws_types": [ "KBaseTrees.Tree" ]
            }
        },
        {
            "id": "save_featuresets",
            "optional": false,
            "advanced": false,
            "allow_multiple": false,
            "default_values": [ "0" ],
            "field_type": "dropdown",
            "dropdown_options": {
                "options": [
                                {
                                        "value": "0",
                                        "display": "DON'T save feature sets",
                                        "id": "save_featuresets-dont",
                                        "ui-name": "save_featuresets-dont"
                                },
                                {
                                        "value": "1",
                                        "display": "DO save feature sets",
                                        "id": "save_featuresets-do",
                                        "ui-name": "save_featuresets-do"
                                }
                ]
            }
        },
        {
            "id": "skip_missing_genomes",
            "optional": false,
            "advanced": true,
            "allow_multiple": false,
            "default_values": [ "1" ],
            "field_type": "dropdown",
            "dropdown_options": {
	    	"options": [
				{
					"value": "1",
					"display": "require all genomes be in Pangenome",
					"id": "show",
					"ui-name": "show"
				},
				{
					"value": "0",
					"display": "ignore genomes not in Pangenome",
					"id": "hide",
					"ui-name": "hide"
				}
		]
            }
        },
        {
            "id": "enforce_genome_version_match",
            "optional": false,
            "advanced": true,
            "allow_multiple": false,
            "default_values": [ "0" ],
            "field_type": "dropdown",
            "dropdown_options": {
	    	"options": [
				{
					"value": "1",
					"display": "require genome version match",
					"id": "show",
					"ui-name": "show"
				},
				{
					"value": "0",
					"display": "use genome version from Species Tree",
					"id": "hide",
					"ui-name": "hide"
				}
		]
            }
        }
    ],
    "behavior": {
        "service-mapping": {
            "url": "",
            "name": "kb_phylogenomics",
            "method": "view_pan_phylo",
            "input_mapping": [
                {
                    "narrative_system_variable": "workspace",
                    "target_property": "workspace_name"
                },
                {
                    "input_parameter": "input_pangenome_ref",
		    "target_property": "input_pangenome_ref",
		    "target_type_transform": "resolved-ref"
                },
                {
                    "input_parameter": "input_speciesTree_ref",
		    "target_property": "input_speciesTree_ref",
		    "target_type_transform": "resolved-ref"
                },
                {
                    "input_parameter": "save_featuresets",
		    "target_property": "save_featuresets"
                },
                {
                    "input_parameter": "skip_missing_genomes",
		    "target_property": "skip_missing_genomes"
                },
                {
                    "input_parameter": "enforce_genome_version_match",
		    "target_property": "enforce_genome_version_match"
                }
            ],
            "output_mapping": [
                {
                    "service_method_output_path": [0, "report_name"],
                    "target_property": "report_name"
                },
                {
                    "service_method_output_path": [0, "report_ref"],
                    "target_property": "report_ref"
                },
                {
                    "narrative_system_variable": "workspace",
                    "target_property": "workspace_name"
                }
            ]
        }
    },
    "job_id_output_field": "docker"
}

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