From 61b6d3a3dd18906422989a551b173b1c9bed78dc Mon Sep 17 00:00:00 2001
From: lgueguen <lgueguen@sb-roscoff.fr>
Date: Wed, 14 Apr 2021 12:16:40 +0200
Subject: [PATCH] Add WF v2 (jbrowse version 1.16.8)

---
 ...load_tripal_synchronize_jbrowse_1org_v2.ga | 459 ++++++++++
 ...load_tripal_synchronize_jbrowse_2org_v2.ga | 815 ++++++++++++++++++
 2 files changed, 1274 insertions(+)
 create mode 100644 workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
 create mode 100644 workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga

diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga b/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
new file mode 100644
index 0000000..0353ae1
--- /dev/null
+++ b/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
@@ -0,0 +1,459 @@
+{
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+    "annotation": "",
+    "format-version": "0.1",
+    "name": "chado_load_tripal_synchronize_jbrowse_1org_v2",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "genome"
+                }
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+            "label": "genome",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 200,
+                "top": 200
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "fa9981ea-4012-40aa-ad84-6e6f61049104",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "5f0bdd95-0f0e-44db-aa40-d1a208322e6f"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "annotations"
+                }
+            ],
+            "label": "annotations",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 200,
+                "top": 290
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "61d23082-b459-4014-8584-6ff5b98ce689",
+            "workflow_outputs": [
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+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "a8ef04db-51ed-4c31-9328-4b13b1a96497"
+                }
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+        "2": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "proteins"
+                }
+            ],
+            "label": "proteins",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 200,
+                "top": 380
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "ea25f583-f55d-4fdd-a7a9-86ffb4b9c731",
+            "workflow_outputs": [
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+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "8d58b06c-796e-42e2-baa6-84b66c4089a5"
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+        },
+        "3": {
+            "annotation": "",
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+            "errors": null,
+            "id": 3,
+            "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": "organism"
+                },
+                {
+                    "description": "runtime parameter for tool Chado load fasta",
+                    "name": "wait_for"
+                }
+            ],
+            "label": null,
+            "name": "Chado load fasta",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "json"
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+            "tool_shed_repository": {
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+                "name": "chado_feature_load_fasta",
+                "owner": "gga",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "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__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+            "type": "tool",
+            "uuid": "a356daf9-f2df-4bbe-9885-e506a676925c",
+            "workflow_outputs": [
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+                    "label": null,
+                    "output_name": "results",
+                    "uuid": "a3213a24-30ee-4f21-a9c5-d8729d95d653"
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+            "annotation": "",
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+            "id": 4,
+            "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": 372
+            },
+            "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__\": \"RuntimeValue\"}}, \"standalone\": \"false\", \"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\": \"\"}}, \"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}",
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+            "workflow_outputs": [
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+                    "output_name": "output",
+                    "uuid": "f9a17b9c-6ed7-4929-81d5-a3ce4bb89a37"
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+            ]
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+                    "output_name": "output"
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+                "gff": {
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+                    "output_name": "output"
+                },
+                "wait_for": {
+                    "id": 3,
+                    "output_name": "results"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Chado load gff",
+                    "name": "analysis_id"
+                },
+                {
+                    "description": "runtime parameter for tool Chado load gff",
+                    "name": "organism"
+                }
+            ],
+            "label": null,
+            "name": "Chado load gff",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "txt"
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+                "top": 194
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+                "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__\": \"ConnectedValue\"}, \"gff\": {\"__class__\": \"ConnectedValue\"}, \"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__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+            "type": "tool",
+            "uuid": "374358c2-1287-4934-9458-4f478884f443",
+            "workflow_outputs": [
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+                    "output_name": "results",
+                    "uuid": "816f0a71-3565-4a90-ba59-ae10e4dd7366"
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+        },
+        "6": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "organisms_0|jbrowse": {
+                    "id": 4,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Add organisms to JBrowse container",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "html"
+                }
+            ],
+            "position": {
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+                "top": 402
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+            "post_job_actions": {},
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+        "7": {
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+            "name": "Synchronize features",
+            "outputs": [
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+                    "type": "txt"
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+            "position": {
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+                "top": 201
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+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
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+                "owner": "gga",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "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}",
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+            "input_connections": {
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+                    "output_name": "results"
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+            "inputs": [],
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+                    "type": "txt"
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+                "top": 200
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+            "tool_shed_repository": {
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+                "owner": "gga",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "tool_state": "{\"mview\": \"\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+            "uuid": "b34ddfee-c317-4c21-99a6-679bd640b1be",
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+            "inputs": [],
+            "label": null,
+            "name": "Index Tripal data",
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+                    "type": "txt"
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+                "top": 200
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+            "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",
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+                "owner": "gga",
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+            "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": "6f8cf6b5-82f2-40bf-80c0-aecf74bedd5a",
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+                    "output_name": "results",
+                    "uuid": "b17408e7-1da6-486c-a355-47693d127df0"
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+    "tags": [],
+    "uuid": "203fda6b-d676-49f0-89e5-f00e3656693d",
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+}
\ No newline at end of file
diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga b/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga
new file mode 100644
index 0000000..14856c5
--- /dev/null
+++ b/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga
@@ -0,0 +1,815 @@
+{
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+    "annotation": "",
+    "format-version": "0.1",
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+    "steps": {
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+            "content_id": null,
+            "errors": null,
+            "id": 0,
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+            "inputs": [
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+                    "name": "genome org1"
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+            "position": {
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+                "top": 200
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "59f823c8-fd7c-441c-84b6-21c367ba12f6",
+            "workflow_outputs": [
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+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "d7c6324d-eac8-452f-a53c-584a418977e6"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "annotations org1"
+                }
+            ],
+            "label": "annotations org1",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 199,
+                "top": 290
+            },
+            "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": "23934081-a6b6-4d25-85ba-3c9c24f19adf"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "proteins org1"
+                }
+            ],
+            "label": "proteins org1",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 200,
+                "top": 385
+            },
+            "tool_id": null,
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+}
\ No newline at end of file
-- 
GitLab