From b9d17f94e212f779b86049624248c189fe8d2a2d Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 11 May 2021 13:41:11 +0200
Subject: [PATCH] Fix missing runtime parameters for blast workflow
---
README.md | 2 +-
...axy-Workflow-load_blast_results_2org_v1.ga | 227 ++++++++++--------
2 files changed, 125 insertions(+), 104 deletions(-)
diff --git a/README.md b/README.md
index bd4d80e..28ff24b 100755
--- a/README.md
+++ b/README.md
@@ -75,7 +75,7 @@ $ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file
```bash
$ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file --workflow workflow_type [-v/--verbose] [OPTIONS]
- --workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "intepro", a couple of preset workflows are available in the workflows_phaeoexplorer directory in this repository)
+ --workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "interpro", a couple of preset workflows are available in the workflows_phaeoexplorer directory in this repository)
--main-directory $PATH (Path where to access stacks; default=current directory)
```
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_2org_v1.ga b/workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_2org_v1.ga
index 67d62db..ba2591c 100644
--- a/workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_2org_v1.ga
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_2org_v1.ga
@@ -20,14 +20,14 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 356.1999969482422,
- "height": 82.19999694824219,
- "left": 168,
- "right": 368,
- "top": 274,
+ "bottom": 230.39999389648438,
+ "height": 61.19999694824219,
+ "left": 97.5,
+ "right": 297.5,
+ "top": 169.1999969482422,
"width": 200,
- "x": 168,
- "y": 274
+ "x": 97.5,
+ "y": 169.1999969482422
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -38,7 +38,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "8c6e3cd8-d0a0-403f-a882-f5206c8627f9"
+ "uuid": "72006174-6297-4777-95bd-ca427b9ea729"
}
]
},
@@ -58,14 +58,14 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 467.1999969482422,
- "height": 82.19999694824219,
- "left": 200,
- "right": 400,
- "top": 385,
+ "bottom": 341.40000915527344,
+ "height": 61.19999694824219,
+ "left": 129.5,
+ "right": 329.5,
+ "top": 280.20001220703125,
"width": 200,
- "x": 200,
- "y": 385
+ "x": 129.5,
+ "y": 280.20001220703125
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -76,7 +76,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "8d7cef33-5fdc-481b-a0fd-542c42c6d032"
+ "uuid": "45971e82-4e85-4993-a9cb-9a4608e9def7"
}
]
},
@@ -96,10 +96,6 @@
"description": "runtime parameter for tool Chado load Blast results",
"name": "analysis_id"
},
- {
- "description": "runtime parameter for tool Chado load Blast results",
- "name": "input"
- },
{
"description": "runtime parameter for tool Chado load Blast results",
"name": "organism_id"
@@ -118,14 +114,14 @@
}
],
"position": {
- "bottom": 361.3999938964844,
- "height": 164.39999389648438,
- "left": 528,
- "right": 728,
- "top": 197,
+ "bottom": 255.8000030517578,
+ "height": 163.60000610351562,
+ "left": 457.5,
+ "right": 657.5,
+ "top": 92.19999694824219,
"width": 200,
- "x": 528,
- "y": 197
+ "x": 457.5,
+ "y": 92.19999694824219
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
@@ -135,7 +131,7 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"blastdb_id\": \"21\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"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_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"blastdb_id\": \"21\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"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": "2.3.4+galaxy0",
"type": "tool",
"uuid": "595f6e1f-955a-42be-b03b-1269d1f7d189",
@@ -143,33 +139,33 @@
{
"label": null,
"output_name": "results",
- "uuid": "c0ad63b8-045e-4a7c-97ba-8bc45862550b"
+ "uuid": "cb238779-29f4-4f22-b6f3-6a8cc84857d1"
}
]
},
"3": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"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 Blast results",
- "name": "input"
+ "description": "runtime parameter for tool Synchronize an analysis",
+ "name": "analysis_id"
},
{
- "description": "runtime parameter for tool Chado load Blast results",
+ "description": "runtime parameter for tool Synchronize an analysis",
"name": "wait_for"
}
],
- "label": "load blast results org2",
- "name": "Chado load Blast results",
+ "label": "sync blast analysis org1",
+ "name": "Synchronize an analysis",
"outputs": [
{
"name": "results",
@@ -177,54 +173,70 @@
}
],
"position": {
- "bottom": 545.3999938964844,
- "height": 164.39999389648438,
- "left": 591,
- "right": 791,
- "top": 381,
+ "bottom": 254.8000030517578,
+ "height": 153.60000610351562,
+ "left": 787.5,
+ "right": 987.5,
+ "top": 101.19999694824219,
"width": 200,
- "x": 591,
- "y": 381
+ "x": 787.5,
+ "y": 101.19999694824219
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
- "changeset_revision": "08ae8b27b193",
- "name": "chado_load_blast",
+ "changeset_revision": "f487ff676088",
+ "name": "tripal_analysis_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": \"1\", \"blastdb_id\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": \"2\", \"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": "2.3.4+galaxy0",
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "5d08ed84-681b-431c-92c9-3b2fd5f32176",
+ "uuid": "c98dedf6-8857-4d23-be94-fe6630f245d7",
"workflow_outputs": [
{
- "label": null,
+ "label": "Synchronize Analysis into Tripal",
"output_name": "results",
- "uuid": "6ed0a7c4-5b78-4016-8c21-0aaa992acd11"
+ "uuid": "1ff4b1db-b6bf-4c48-a0ab-0a8513683999"
}
]
},
"4": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"errors": null,
"id": 4,
"input_connections": {
+ "input": {
+ "id": 1,
+ "output_name": "output"
+ },
"wait_for": {
- "id": 2,
+ "id": 3,
"output_name": "results"
}
},
"inputs": [
{
- "description": "runtime parameter for tool Synchronize an analysis",
+ "description": "runtime parameter for tool Chado load Blast results",
"name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load Blast results",
+ "name": "input"
+ },
+ {
+ "description": "runtime parameter for tool Chado load Blast results",
+ "name": "organism_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load Blast results",
+ "name": "wait_for"
}
],
- "label": "sync blast analysis org1",
- "name": "Synchronize an analysis",
+ "label": "load blast results org2",
+ "name": "Chado load Blast results",
"outputs": [
{
"name": "results",
@@ -232,32 +244,32 @@
}
],
"position": {
- "bottom": 360.3999938964844,
- "height": 154.39999389648438,
- "left": 858,
- "right": 1058,
- "top": 206,
+ "bottom": 439.8000183105469,
+ "height": 163.60000610351562,
+ "left": 520.5,
+ "right": 720.5,
+ "top": 276.20001220703125,
"width": 200,
- "x": 858,
- "y": 206
+ "x": 520.5,
+ "y": 276.20001220703125
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"tool_shed_repository": {
- "changeset_revision": "f487ff676088",
- "name": "tripal_analysis_sync",
+ "changeset_revision": "08ae8b27b193",
+ "name": "chado_load_blast",
"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",
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"blastdb_id\": \"21\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"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": "2.3.4+galaxy0",
"type": "tool",
- "uuid": "99e7496d-ac32-467d-8c09-2efd48d0231a",
+ "uuid": "a7ec5c91-7cef-4b9f-95a0-ed5542b8e142",
"workflow_outputs": [
{
- "label": "Synchronize Analysis into Tripal",
+ "label": null,
"output_name": "results",
- "uuid": "9792ea7a-0b4d-4355-9ce6-db2ba1ed36e9"
+ "uuid": "119f219e-3d80-4b42-bb38-d07d4583048c"
}
]
},
@@ -268,11 +280,20 @@
"id": 5,
"input_connections": {
"wait_for": {
- "id": 3,
+ "id": 4,
"output_name": "results"
}
},
- "inputs": [],
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Synchronize an analysis",
+ "name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Synchronize an analysis",
+ "name": "wait_for"
+ }
+ ],
"label": "sync blast analysis org2",
"name": "Synchronize an analysis",
"outputs": [
@@ -282,14 +303,14 @@
}
],
"position": {
- "bottom": 545.3999938964844,
- "height": 154.39999389648438,
- "left": 899,
- "right": 1099,
- "top": 391,
+ "bottom": 440.8000183105469,
+ "height": 153.60000610351562,
+ "left": 828.5,
+ "right": 1028.5,
+ "top": 287.20001220703125,
"width": 200,
- "x": 899,
- "y": 391
+ "x": 828.5,
+ "y": 287.20001220703125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
@@ -299,15 +320,15 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": \"1\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "99f68436-37c7-409a-bcf0-70bde40a9a8e",
+ "uuid": "2fff7637-7904-46ff-87e1-ce2721727e75",
"workflow_outputs": [
{
"label": "Synchronize Analysis into Tripal",
"output_name": "results",
- "uuid": "ce2c98b7-17f2-4646-a3bf-784af0103f4e"
+ "uuid": "924991f3-6dd4-4752-9ce2-3832d72dff57"
}
]
},
@@ -332,14 +353,14 @@
}
],
"position": {
- "bottom": 474.3999938964844,
- "height": 154.39999389648438,
- "left": 1174,
- "right": 1374,
- "top": 320,
+ "bottom": 368.8000030517578,
+ "height": 153.60000610351562,
+ "left": 1103.5,
+ "right": 1303.5,
+ "top": 215.1999969482422,
"width": 200,
- "x": 1174,
- "y": 320
+ "x": 1103.5,
+ "y": 215.1999969482422
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
@@ -357,7 +378,7 @@
{
"label": "Populate Tripal materialized view(s)",
"output_name": "results",
- "uuid": "31970b1e-e567-4994-b05e-31d3406ebdf3"
+ "uuid": "dc519305-8c27-4c53-9150-7dd37b5090cd"
}
]
},
@@ -382,14 +403,14 @@
}
],
"position": {
- "bottom": 454.6000061035156,
- "height": 113.60000610351562,
- "left": 1444,
- "right": 1644,
- "top": 341,
+ "bottom": 349,
+ "height": 112.80000305175781,
+ "left": 1373.5,
+ "right": 1573.5,
+ "top": 236.1999969482422,
"width": 200,
- "x": 1444,
- "y": 341
+ "x": 1373.5,
+ "y": 236.1999969482422
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
@@ -407,12 +428,12 @@
{
"label": "Index Tripal data",
"output_name": "results",
- "uuid": "c4398cf0-10ca-45c7-ab62-9854b7519ecb"
+ "uuid": "e2911922-2412-4618-97fe-bcc783bb0865"
}
]
}
},
"tags": [],
- "uuid": "1219fcfa-e57c-437e-ac5e-4d803e3dafd9",
- "version": 5
+ "uuid": "ffae97b5-698a-41a5-8561-470300594544",
+ "version": 6
}
\ No newline at end of file
--
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