{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Jbrowse", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 200 }, "tool_id": null, "tool_state": "{\"optional\": false}", "tool_version": null, "type": "data_input", "uuid": "751caac1-d015-4d77-8a68-2c3debae0caf", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "ac834ebd-236e-4539-86da-916da1ac8c5a" } ] }, "1": { "annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 290 }, "tool_id": null, "tool_state": "{\"optional\": false}", "tool_version": null, "type": "data_input", "uuid": "5cb81c38-64fe-4bdc-9043-bd862bdefc6d", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "a9c468b7-935b-49b3-83d0-6eabafae8daf" } ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0", "errors": null, "id": 2, "input_connections": { "reference_genome|genome": { "id": 0, "output_name": "output" }, "track_groups_0|data_tracks_0|data_format|annotation": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool JBrowse", "name": "reference_genome" } ], "label": null, "name": "JBrowse", "outputs": [ { "name": "output", "type": "html" } ], "position": { "left": 486, "top": 200 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0", "tool_shed_repository": { "changeset_revision": "8774b28235bb", "name": "jbrowse", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"test\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"test\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"mRNA\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": \"{{ MENU_URL }}\", \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.16.10+galaxy0", "type": "tool", "uuid": "ba7d15fd-8ffd-407d-9a45-47cd4be68bd2", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "519355d7-82cc-47f0-a96c-3ee0e39aa7df" } ] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1", "errors": null, "id": 3, "input_connections": { "organisms_0|jbrowse": { "id": 2, "output_name": "output" } }, "inputs": [], "label": null, "name": "Add organisms to JBrowse container", "outputs": [ { "name": "output", "type": "html" } ], "position": { "left": 772, "top": 200 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1", "tool_shed_repository": { "changeset_revision": "11033bdad2ca", "name": "jbrowse_to_container", "owner": "gga", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"advanced\": {\"unique_id\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.5.1", "type": "tool", "uuid": "1cf25ca3-2287-4b82-9e93-b8828eed70a2", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "f78c7496-18a9-4c47-ad7f-a3ac31456749" } ] } }, "tags": [], "uuid": "77f04b69-2dec-430b-891f-f4ddbf04d1db", "version": 1 }