{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "Chado load Tripal synchronize",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 227
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "89e7487e-004d-4db1-b5eb-1676b98aebde",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "08f77326-1435-4fad-a610-e56f06a0ced5"
}
]
},
"1": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 317
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "1d25f54c-7575-4c8d-be55-73dd7e58613f",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "e8f16746-c91f-4147-b460-f1052650e699"
}
]
},
"2": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 2,
"input_connections": {},
"inputs": [],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 407
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "98ade546-95a4-477c-bd19-38d278849b98"
}
]
},
"3": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 3,
"input_connections": {},
"inputs": [],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 497
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "41417aad-64e5-4480-9c36-842d0dda1c6d"
}
]
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"errors": null,
"id": 4,
"input_connections": {
"fasta": {
"id": 0,
"output_name": "output"
},
"wait_for": {
"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": "organism"
}
],
"label": null,
"name": "Chado load fasta",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"left": 486,
"top": 227
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"tool_shed_repository": {
"changeset_revision": "a7ab30ded37d",
"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__\": \"ConnectedValue\"}, \"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__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.3",
"type": "tool",
"uuid": "f7a44182-3620-4a19-9e67-94fe584d4206",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "24ed7255-b4a6-4000-b82b-c18d81822262"
}
]
},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"errors": null,
"id": 5,
"input_connections": {
"fasta": {
"id": 2,
"output_name": "output"
},
"gff": {
"id": 1,
"output_name": "output"
},
"wait_for": {
"id": 4,
"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": null,
"name": "Chado load gff",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"left": 772,
"top": 227
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"tool_shed_repository": {
"changeset_revision": "6fdfbf0caa8c",
"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\": \"protein\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.3",
"type": "tool",
"uuid": "b100a055-0dab-4f2f-8c46-573713ed3fff",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "d0ce6d85-fb8b-4509-9784-a8ded1aeae05"
}
]
},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
"errors": null,
"id": 6,
"input_connections": {
"wait_for": {
"id": 5,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize an organism",
"name": "organism_id"
}
],
"label": null,
"name": "Synchronize an organism",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"left": 1058,
"top": 227
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "afd5d92745fb",
"name": "tripal_organism_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "040183a5-1aba-4bf6-9669-c6e93cfff3ea",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "f1f2dc7a-37e2-4bd3-b997-8f1e3eed11aa"
}
]
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"errors": null,
"id": 7,
"input_connections": {
"wait_for": {
"id": 6,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize an analysis",
"name": "analysis_id"
}
],
"label": null,
"name": "Synchronize an analysis",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"left": 1344,
"top": 227
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "f487ff676088",
"name": "tripal_analysis_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "6096e174-c85d-4e50-916f-a396d58a909b",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "a309f4e4-3402-4eb5-8b70-1acfa1f26bb4"
}
]
},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"errors": null,
"id": 8,
"input_connections": {
"wait_for": {
"id": 7,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize an analysis",
"name": "analysis_id"
}
],
"label": null,
"name": "Synchronize an analysis",
"outputs": [
{
"name": "results",
"type": "json"
}
],
"position": {
"left": 1630,
"top": 227
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "f487ff676088",
"name": "tripal_analysis_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "d6072bb6-036d-4fbf-893c-d25f139a05ac",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "ff817e04-d0ce-461f-a97a-843e36a25aca"
}
]
},
"9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"errors": null,
"id": 9,
"input_connections": {
"wait_for": {
"id": 8,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize features",
"name": "organism_id"
}
],
"label": null,
"name": "Synchronize features",
"outputs": [
{
"name": "results",
"type": "txt"
}
],
"position": {
"left": 1916,
"top": 227
},
"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": "9d39d394-7375-4187-86f3-6dc676c9ca30",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
"uuid": "5047a899-60e2-4acc-a95f-4f60f83c32ae"
}
]
}
},
"tags": [],
"uuid": "00c4d6e1-f470-4b31-9cc1-402aa9b598e2",
"version": 1
}