From 27cd39b8c5e42dbe44190d55caa6f55b4cd46805 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 31 May 2021 12:33:38 +0200
Subject: [PATCH] Update to wf_v6
---
constants_phaeo.py | 8 +-
...load_tripal_synchronize_jbrowse_1org_v6.ga | 519 ++++++++++
...load_tripal_synchronize_jbrowse_2org_v6.ga | 887 ++++++++++++++++++
3 files changed, 1410 insertions(+), 4 deletions(-)
create mode 100644 workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga
create mode 100644 workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga
diff --git a/constants_phaeo.py b/constants_phaeo.py
index 10cdb8c..ace8d66 100644
--- a/constants_phaeo.py
+++ b/constants_phaeo.py
@@ -9,7 +9,7 @@ import constants
WORKFLOWS_PATH = "workflows_phaeoexplorer/"
WF_LOAD_GFF_JB = "load_fasta_gff_jbrowse"
-WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v4.ga"
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga"
WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME = "0"
WF_LOAD_GFF_JB_1_ORG_INPUT_GFF = "1"
WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS = "2"
@@ -21,9 +21,9 @@ WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
-WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v4.ga"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "0"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "1"
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "0"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "1"
WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "3"
WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "4"
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga
new file mode 100644
index 0000000..d9dae22
--- /dev/null
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga
@@ -0,0 +1,519 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "chado_load_tripal_synchronize_jbrowse_1org_v6",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "genome"
+ }
+ ],
+ "label": "genome",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 365.8000030517578,
+ "height": 61.80000305175781,
+ "left": 176.5,
+ "right": 376.5,
+ "top": 304,
+ "width": 200,
+ "x": 176.5,
+ "y": 304
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "40c1e307-2cc6-4914-aebc-76373131708d",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "42803cc3-a5cc-44e9-b6c8-2456472579cd"
+ }
+ ]
+ },
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+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "annotations"
+ }
+ ],
+ "label": "annotations",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 455.8000030517578,
+ "height": 61.80000305175781,
+ "left": 207.5,
+ "right": 407.5,
+ "top": 394,
+ "width": 200,
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+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
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+ "2": {
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+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
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+ "description": "",
+ "name": "proteins"
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+ ],
+ "label": "proteins",
+ "name": "Input dataset",
+ "outputs": [],
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+ "height": 61.80000305175781,
+ "left": 229.5,
+ "right": 429.5,
+ "top": 483,
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+ "tool_state": "{\"optional\": false}",
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+ "uuid": "018cd90b-1f34-4d37-9919-7767c8c3026d",
+ "workflow_outputs": [
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+ "output_name": "output",
+ "uuid": "8623782b-77e2-4eea-bb20-0cf158a503ff"
+ }
+ ]
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+ "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"
+ }
+ ],
+ "position": {
+ "bottom": 445,
+ "height": 144,
+ "left": 506.5,
+ "right": 706.5,
+ "top": 301,
+ "width": 200,
+ "x": 506.5,
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+ "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__\": \"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}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "59bb1c33-b93f-49db-941d-66cbdaaf2cb5",
+ "workflow_outputs": [
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+ "output_name": "results",
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+ },
+ "4": {
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+ "errors": null,
+ "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": {
+ "bottom": 681.1999969482422,
+ "height": 205.1999969482422,
+ "left": 493.5,
+ "right": 693.5,
+ "top": 476,
+ "width": 200,
+ "x": 493.5,
+ "y": 476
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "4542035c1075",
+ "name": "jbrowse",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
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+ "tool_version": null,
+ "type": "tool",
+ "uuid": "212e883c-daeb-4b4f-9bed-c90f130da794",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "38052de9-61ed-4cdd-8a11-1b1d6dd8a8e6"
+ }
+ ]
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+ "5": {
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+ "fasta": {
+ "id": 2,
+ "output_name": "output"
+ },
+ "gff": {
+ "id": 1,
+ "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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+ "name": "chado_feature_load_gff",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
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+ "output_name": "output"
+ }
+ },
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+ "label": null,
+ "name": "Add organisms to JBrowse container",
+ "outputs": [
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+ "type": "html"
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+ "height": 134,
+ "left": 779.5,
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+ "name": "jbrowse_to_container",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
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+ "type": "txt"
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+ "tool_version": null,
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+ "tags": [],
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+}
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diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga
new file mode 100644
index 0000000..854b4b4
--- /dev/null
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga
@@ -0,0 +1,887 @@
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