Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • abims/e-infra/gga_load_data
1 result
Show changes
Commits on Source (5)
Expand all Hide whitespace changes
Inline Side-by-side
run_workflow_phaeoexplorer.py
View file @ 23e250bb
This diff is collapsed.
workflows_phaeoexplorer/Galaxy-Workflow-load_interproscan_1org_v1.ga 0 → 100644
View file @ 23e250bb
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "load_inteproscan_1org1_v1",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "inteproscan file org1"
}
],
"label": "inteproscan file org1",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 319.1999969482422,
"height": 82.19999694824219,
"left": 287,
"right": 487,
"top": 237,
"width": 200,
"x": 287,
"y": 237
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "3b13466d-1b81-475a-b652-183ed9d24bfa",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "aff82f29-1971-4283-bfe8-cdab4857a215"
}
]
},
"1": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"errors": null,
"id": 1,
"input_connections": {
"input": {
"id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "input"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "organism_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "wait_for"
}
],
"label": "interproscan load org 1",
"name": "Chado load InterProScan results",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"bottom": 371.3999938964844,
"height": 164.39999389648438,
"left": 595,
"right": 795,
"top": 207,
"width": 200,
"x": 595,
"y": 207
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"tool_shed_repository": {
"changeset_revision": "1e54f2717e74",
"name": "chado_load_interpro",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"parse_go\": \"false\", \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"query_type\": \"polypeptide\", \"re_name\": \"\", \"skip_missing\": \"false\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.6+galaxy0",
"type": "tool",
"uuid": "a084abdc-a0f4-4670-a486-4aed4e0f61fa",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "dbaab44d-1494-4fbe-bd15-455f7cbf7307"
}
]
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
"errors": null,
"id": 2,
"input_connections": {
"wait_for": {
"id": 1,
"output_name": "results"
}
},
"inputs": [],
"label": null,
"name": "Populate materialized views",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 360.3999938964844,
"height": 154.39999389648438,
"left": 876,
"right": 1076,
"top": 206,
"width": 200,
"x": 876,
"y": 206
},
"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": "2acbe412-1318-46e8-a178-72f50df36a07",
"workflow_outputs": [
{
"label": "Populate Tripal materialized view(s)",
"output_name": "results",
"uuid": "08a4eec2-b95a-4c75-8116-b0fc9477812f"
}
]
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
"errors": null,
"id": 3,
"input_connections": {
"wait_for": {
"id": 2,
"output_name": "results"
}
},
"inputs": [],
"label": null,
"name": "Index Tripal data",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 340.6000061035156,
"height": 113.60000610351562,
"left": 1150,
"right": 1350,
"top": 227,
"width": 200,
"x": 1150,
"y": 227
},
"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": "42d782ff-9e6b-49d8-bd17-37dc67f31a18",
"workflow_outputs": [
{
"label": "Index Tripal data",
"output_name": "results",
"uuid": "8b38b48f-5d4e-49e6-ad70-748ad64dc901"
}
]
}
},
"tags": [],
"uuid": "9912daac-c00e-4d5e-a93e-a747bd1b3499",
"version": 3
}
\ No newline at end of file
workflows_phaeoexplorer/Galaxy-Workflow-load_interproscan_2org_v1.ga 0 → 100644
View file @ 23e250bb
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "load_interproscan_2org_v1",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "interproscan file org 1"
}
],
"label": "interproscan file org 1",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 350.1999969482422,
"height": 82.19999694824219,
"left": 414,
"right": 614,
"top": 268,
"width": 200,
"x": 414,
"y": 268
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "bfce9a38-df8a-46ef-af2e-390a4982ebfc",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "d5d96afa-8dcc-4322-89fa-df56fd503d89"
}
]
},
"1": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "interproscan file org 2"
}
],
"label": "interproscan file org 2",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 451.1999969482422,
"height": 82.19999694824219,
"left": 437,
"right": 637,
"top": 369,
"width": 200,
"x": 437,
"y": 369
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "45f57c7f-f08c-4b3b-879d-1acd246868fb",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "f5e4ae10-fdbf-47e9-99d8-0644bf8bb46f"
}
]
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"errors": null,
"id": 2,
"input_connections": {
"input": {
"id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "input"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "organism_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "wait_for"
}
],
"label": "inteproscan load org 1",
"name": "Chado load InterProScan results",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"bottom": 365.3999938964844,
"height": 164.39999389648438,
"left": 790,
"right": 990,
"top": 201,
"width": 200,
"x": 790,
"y": 201
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"tool_shed_repository": {
"changeset_revision": "1e54f2717e74",
"name": "chado_load_interpro",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"parse_go\": \"false\", \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"query_type\": \"polypeptide\", \"re_name\": \"\", \"skip_missing\": \"false\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.6+galaxy0",
"type": "tool",
"uuid": "e6c509b4-ea16-4fda-b171-3dc781a54759",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "bfff8893-5c92-45a0-88ca-594b33a8b4e2"
}
]
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"errors": null,
"id": 3,
"input_connections": {
"input": {
"id": 1,
"output_name": "output"
},
"wait_for": {
"id": 2,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "input"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "organism_id"
},
{
"description": "runtime parameter for tool Chado load InterProScan results",
"name": "wait_for"
}
],
"label": "interproscan load org 2",
"name": "Chado load InterProScan results",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"bottom": 555.3999938964844,
"height": 164.39999389648438,
"left": 819,
"right": 1019,
"top": 391,
"width": 200,
"x": 819,
"y": 391
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_interpro/load_interpro/2.3.6+galaxy0",
"tool_shed_repository": {
"changeset_revision": "1e54f2717e74",
"name": "chado_load_interpro",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"parse_go\": \"false\", \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"query_type\": \"polypeptide\", \"re_name\": \"\", \"skip_missing\": \"false\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.6+galaxy0",
"type": "tool",
"uuid": "1832aceb-851c-4020-9c07-8193e8b2299a",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "be9f442f-7f19-4b84-94cf-9c2c28d9a6a5"
}
]
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
"errors": null,
"id": 4,
"input_connections": {
"wait_for": {
"id": 3,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Populate materialized views",
"name": "wait_for"
}
],
"label": null,
"name": "Populate materialized views",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 459.3999938964844,
"height": 154.39999389648438,
"left": 1118,
"right": 1318,
"top": 305,
"width": 200,
"x": 1118,
"y": 305
},
"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__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "a819f33b-e566-43e5-a467-e3410ce431ec",
"workflow_outputs": [
{
"label": "Populate Tripal materialized view(s)",
"output_name": "results",
"uuid": "96483655-995e-4d4e-b8c6-7f602c974ee3"
}
]
},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
"errors": null,
"id": 5,
"input_connections": {
"wait_for": {
"id": 4,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Index Tripal data",
"name": "wait_for"
}
],
"label": null,
"name": "Index Tripal data",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"bottom": 442.6000061035156,
"height": 113.60000610351562,
"left": 1382,
"right": 1582,
"top": 329,
"width": 200,
"x": 1382,
"y": 329
},
"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__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.1",
"type": "tool",
"uuid": "489483da-c7c7-49a5-b5d4-353db41b1240",
"workflow_outputs": [
{
"label": "Index Tripal data",
"output_name": "results",
"uuid": "3df4fd46-5dd9-49d6-b0d2-24425d9ba91e"
}
]
}
},
"tags": [],
"uuid": "ac96d70e-60b6-4455-8d14-9219d0674950",
"version": 1
}
\ No newline at end of file