Skip to content
Snippets Groups Projects
Commit cb7db4d8 authored by Arthur Le Bars's avatar Arthur Le Bars
Browse files

Worfklow 2 organisms v3

parent a1d874e2
No related branches found
No related tags found
2 merge requests!9Release 2.0 (merge dev to master),!5Workflow v2
Hide whitespace changes
Inline Side-by-side
run_workflow_phaeoexplorer.py
+ 2
− 2
View file @ cb7db4d8
...@@ -1049,7 +1049,7 @@ if __name__ == "__main__": ...@@ -1049,7 +1049,7 @@ if __name__ == "__main__":
logging.info("Input organism %s: 2 species detected in input dictionary" % k) logging.info("Input organism %s: 2 species detected in input dictionary" % k)
# Set workflow path (2 organisms) # Set workflow path (2 organisms)
workflow_path = os.path.join(os.path.abspath(script_dir), "workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga") workflow_path = os.path.join(os.path.abspath(script_dir), "workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v3.ga")
# Instance object required variables # Instance object required variables
instance_url, email, password = None, None, None instance_url, email, password = None, None, None
...@@ -1202,7 +1202,7 @@ if __name__ == "__main__": ...@@ -1202,7 +1202,7 @@ if __name__ == "__main__":
workflow_dict["steps"]["10"]["tool_state"] = workflow_dict["steps"]["10"]["tool_state"].replace("__FULL_NAME_ORG2__", org2_full_name).replace("__UNIQUE_ID_ORG2__", org2_species_folder_name) workflow_dict["steps"]["10"]["tool_state"] = workflow_dict["steps"]["10"]["tool_state"].replace("__FULL_NAME_ORG2__", org2_full_name).replace("__UNIQUE_ID_ORG2__", org2_species_folder_name)
print(workflow_dict) print(workflow_dict)
# Import the workflow in galaxy as a dict # Import the workflow in galaxy as a dict
instance.workflows.import_workflow_dict(workflow_dict=workflow_dict) instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
......
workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v3.ga 0 → 100644
+ 907
− 0
View file @ cb7db4d8
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "chado_load_tripal_synchronize_jbrowse_2org_v2",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "genome org1"
}
],
"label": "genome org1",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 204.8000030517578,
"height": 61.80000305175781,
"left": 215,
"right": 415,
"top": 143,
"width": 200,
"x": 215,
"y": 143
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "59f823c8-fd7c-441c-84b6-21c367ba12f6",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "95cc9784-0f9c-46df-9f62-4c342f6695e7"
}
]
},
"1": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "annotations org1"
}
],
"label": "annotations org1",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 294.8000030517578,
"height": 61.80000305175781,
"left": 214,
"right": 414,
"top": 233,
"width": 200,
"x": 214,
"y": 233
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "c82b756f-2ef5-41d5-9e14-eb9a7ef942c7",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "b67afacf-2d88-49f6-af15-02500f0ddc90"
}
]
},
"2": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 2,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "proteins org1"
}
],
"label": "proteins org1",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 389.8000030517578,
"height": 61.80000305175781,
"left": 215,
"right": 415,
"top": 328,
"width": 200,
"x": 215,
"y": 328
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "0a0ac416-68b8-4c48-980e-04c6230c721e",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "cc50348e-1372-406e-9b3e-d2cacfea81b2"
}
]
},
"3": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 3,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "genome org2"
}
],
"label": "genome org2",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 479.8000030517578,
"height": 61.80000305175781,
"left": 214,
"right": 414,
"top": 418,
"width": 200,
"x": 214,
"y": 418
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "ddd5f0f8-9e14-42f0-a866-2971d02e5435",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "0f63af8f-7c12-4c7a-a491-4f55f65fff4e"
}
]
},
"4": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 4,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "annotations org2"
}
],
"label": "annotations org2",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 573.8000030517578,
"height": 61.80000305175781,
"left": 216,
"right": 416,
"top": 512,
"width": 200,
"x": 216,
"y": 512
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "c7f3b553-5cd2-46e6-a792-e864ab0d2459",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "e5ec0e3f-c56a-4c4c-b905-26b7e85808d3"
}
]
},
"5": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 5,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "proteins org2"
}
],
"label": "proteins org2",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 663.8000030517578,
"height": 61.80000305175781,
"left": 217,
"right": 417,
"top": 602,
"width": 200,
"x": 217,
"y": 602
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "b5b82a8a-f73c-4183-bc0a-6956e5ad9d0a",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "92d17a84-9137-4437-add9-5b3e551bb6b2"
}
]
},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
"fasta": {
"id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load fasta",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "fasta"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "organism"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "wait_for"
}
],
"label": "Chado load fasta org",
"name": "Chado load fasta",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"bottom": 307.3999938964844,
"height": 164.39999389648438,
"left": 501,
"right": 701,
"top": 143,
"width": 200,
"x": 501,
"y": 143
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "ba4d07fbaf47",
"name": "chado_feature_load_fasta",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.4+galaxy0",
"type": "tool",
"uuid": "d15253d8-a673-4bfb-8051-e06d6017288e",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "c5b2da92-4326-46c1-94cb-e0301e2629f8"
}
]
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
"errors": null,
"id": 7,
"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": [],
"label": "JBrowse org1",
"name": "JBrowse",
"outputs": [
{
"name": "output",
"type": "html"
}
],
"position": {
"bottom": 868.1999969482422,
"height": 205.1999969482422,
"left": 513,
"right": 713,
"top": 663,
"width": 200,
"x": 513,
"y": 663
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fd5dbf0f732e",
"name": "jbrowse",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"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__\": \"ConnectedValue\"}}, \"standalone\": \"false\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"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\": \"\"}}, \"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\": {\"__class__\": \"RuntimeValue\"}, \"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": "1.16.8+galaxy1",
"type": "tool",
"uuid": "16f56647-e3c0-4bda-a126-9011cd3115b8",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "0a865401-1041-44b8-bd20-2c422bc695fa"
}
]
},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
"errors": null,
"id": 8,
"input_connections": {
"reference_genome|genome": {
"id": 3,
"output_name": "output"
},
"track_groups_0|data_tracks_0|data_format|annotation": {
"id": 4,
"output_name": "output"
}
},
"inputs": [],
"label": "JBrowse org2",
"name": "JBrowse",
"outputs": [
{
"name": "output",
"type": "html"
}
],
"position": {
"bottom": 1084.1999969482422,
"height": 205.1999969482422,
"left": 518,
"right": 718,
"top": 879,
"width": 200,
"x": 518,
"y": 879
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fd5dbf0f732e",
"name": "jbrowse",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"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__\": \"ConnectedValue\"}}, \"standalone\": \"false\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"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\": \"\"}}, \"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\": {\"__class__\": \"RuntimeValue\"}, \"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": "1.16.8+galaxy1",
"type": "tool",
"uuid": "f4525181-f8b3-47ab-979f-fee0f46f13ba",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "4acd10c7-ef6d-4808-8aac-253d91733853"
}
]
},
"9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
"errors": null,
"id": 9,
"input_connections": {
"fasta": {
"id": 2,
"output_name": "output"
},
"gff": {
"id": 1,
"output_name": "output"
},
"wait_for": {
"id": 6,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load gff",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "fasta"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "gff"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "organism"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "wait_for"
}
],
"label": "Chado load gff ",
"name": "Chado load gff",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 317.3999938964844,
"height": 174.39999389648438,
"left": 787,
"right": 987,
"top": 143,
"width": 200,
"x": 787,
"y": 143
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "e9a6d7568817",
"name": "chado_feature_load_gff",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(_.+)$\", \"re_protein\": \"prot\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.4+galaxy0",
"type": "tool",
"uuid": "281d98df-9a07-4beb-b3e8-a1ac72d8c0c9",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "e92a76f7-7b7e-429c-9aa7-cfc8ce5f0cd1"
}
]
},
"10": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
"errors": null,
"id": 10,
"input_connections": {
"organisms_0|jbrowse": {
"id": 7,
"output_name": "output"
},
"organisms_1|jbrowse": {
"id": 8,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "Add organisms to JBrowse container",
"outputs": [
{
"name": "output",
"type": "html"
}
],
"position": {
"bottom": 995.8000030517578,
"height": 184.8000030517578,
"left": 883,
"right": 1083,
"top": 811,
"width": 200,
"x": 883,
"y": 811
},
"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\"}}}, {\"__index__\": 1, \"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": "0f70a2d4-f599-4514-846d-16a558251a9a",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "0e8e64c8-7dc6-46f1-aca2-d4a6ffce638b"
}
]
},
"11": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"errors": null,
"id": 11,
"input_connections": {
"wait_for": {
"id": 9,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize features",
"name": "organism_id"
}
],
"label": "Synchronize features org1",
"name": "Synchronize features",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 300.3999938964844,
"height": 154.39999389648438,
"left": 1069,
"right": 1269,
"top": 146,
"width": 200,
"x": 1069,
"y": 146
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "64e36c3f0dd6",
"name": "tripal_feature_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"polypeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "7ed6c0a0-f36b-4a57-9fd8-4900af93b39c",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "ddd66d56-b81b-4ad7-a96d-baf365d8b85a"
}
]
},
"12": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"errors": null,
"id": 12,
"input_connections": {
"fasta": {
"id": 3,
"output_name": "output"
},
"wait_for": {
"id": 11,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load fasta",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "fasta"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "organism"
},
{
"description": "runtime parameter for tool Chado load fasta",
"name": "wait_for"
}
],
"label": "Chado load fasta org2",
"name": "Chado load fasta",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"bottom": 562.3999938964844,
"height": 164.39999389648438,
"left": 514,
"right": 714,
"top": 398,
"width": 200,
"x": 514,
"y": 398
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "ba4d07fbaf47",
"name": "chado_feature_load_fasta",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.4+galaxy0",
"type": "tool",
"uuid": "049f96ea-620a-434c-b32a-886cac9174ef",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "e67a8a18-2a9d-4906-8960-3d76455de221"
}
]
},
"13": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
"errors": null,
"id": 13,
"input_connections": {
"fasta": {
"id": 5,
"output_name": "output"
},
"gff": {
"id": 4,
"output_name": "output"
},
"wait_for": {
"id": 12,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load gff",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "fasta"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "gff"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "organism"
},
{
"description": "runtime parameter for tool Chado load gff",
"name": "wait_for"
}
],
"label": "Chado load gff org2",
"name": "Chado load gff",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 594.8000030517578,
"height": 194.8000030517578,
"left": 799,
"right": 999,
"top": 400,
"width": 200,
"x": 799,
"y": 400
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "e9a6d7568817",
"name": "chado_feature_load_gff",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(_.+)$\", \"re_protein\": \"prot\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.4+galaxy0",
"type": "tool",
"uuid": "9293d4b6-7cad-4d6b-8143-e134f58c75fe",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "975db068-46e0-4c0a-a74f-80c7d2137ac8"
}
]
},
"14": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"errors": null,
"id": 14,
"input_connections": {
"wait_for": {
"id": 13,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize features",
"name": "organism_id"
}
],
"label": "Synchronize features org2",
"name": "Synchronize features",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 560.3999938964844,
"height": 154.39999389648438,
"left": 1078,
"right": 1278,
"top": 406,
"width": 200,
"x": 1078,
"y": 406
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "64e36c3f0dd6",
"name": "tripal_feature_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"polypeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "090a12c8-f931-4f3c-8853-9ae581c7c091",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "f51aa0a5-e2f8-41af-bb56-dbfe220e7fc8"
}
]
},
"15": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
"errors": null,
"id": 15,
"input_connections": {
"wait_for": {
"id": 14,
"output_name": "results"
}
},
"inputs": [],
"label": null,
"name": "Populate materialized views",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 456.3999938964844,
"height": 154.39999389648438,
"left": 1362,
"right": 1562,
"top": 302,
"width": 200,
"x": 1362,
"y": 302
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "3c08f32a3dc1",
"name": "tripal_db_populate_mviews",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"mview\": \"\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "0a3bd8c6-240b-45f6-a90d-e88ff3703fa7",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "c7229bc3-fbe7-4c7f-9a08-8ad631d57766"
}
]
},
"16": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
"errors": null,
"id": 16,
"input_connections": {
"wait_for": {
"id": 15,
"output_name": "results"
}
},
"inputs": [],
"label": null,
"name": "Index Tripal data",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 416.6000061035156,
"height": 113.60000610351562,
"left": 1638,
"right": 1838,
"top": 303,
"width": 200,
"x": 1638,
"y": 303
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
"tool_shed_repository": {
"changeset_revision": "d55a39f12dda",
"name": "tripal_db_index",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"expose\": {\"do_expose\": \"no\", \"__current_case__\": 0}, \"queues\": \"10\", \"table\": {\"mode\": \"website\", \"__current_case__\": 0}, \"tokenizer\": \"standard\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.1",
"type": "tool",
"uuid": "b01a554e-a43a-494e-876c-ebe134c4c48f",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "0547bccc-451b-4de1-9452-83fe86d8bc2a"
}
]
}
},
"tags": [],
"uuid": "ef44b9b7-f9df-454e-bbba-070299d056d1",
"version": 1
}
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment