# HG changeset patch
# User tduigou
# Date 1639583959 0
# Node ID 7d42adefc60aff1aa17808f1eaa2ccb5cc878298
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
diff -r 000000000000 -r 7d42adefc60a BASIC_Assembly_Workflow.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BASIC_Assembly_Workflow.ga Wed Dec 15 15:59:19 2021 +0000
@@ -0,0 +1,259 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "BASIC_Assembly_Workflow",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "SBML pathways"
+ }
+ ],
+ "label": "SBML pathways",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 335.8000030517578,
+ "height": 61.80000305175781,
+ "left": -118.5,
+ "right": 81.5,
+ "top": 274,
+ "width": 200,
+ "x": -118.5,
+ "y": 274
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "274db529-8d38-4f2b-84ce-8bc14e5fc35e",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "0058aece-8f90-4470-ba24-ba9cf7a08fdc"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0",
+ "errors": null,
+ "id": 1,
+ "input_connections": {
+ "pathway": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Selenzyme",
+ "outputs": [
+ {
+ "name": "uniprot_ids",
+ "type": "xml"
+ },
+ {
+ "name": "uniprot_ids_csv",
+ "type": "csv"
+ }
+ ],
+ "position": {
+ "bottom": 464.6000061035156,
+ "height": 123.60000610351562,
+ "left": 117.5,
+ "right": 317.5,
+ "top": 341,
+ "width": 200,
+ "x": 117.5,
+ "y": 341
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0",
+ "tool_shed_repository": {
+ "changeset_revision": "481f7c35323d",
+ "name": "selenzy",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\", \"taxonIDs\": \"83333\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "0.1.0",
+ "type": "tool",
+ "uuid": "b8f4e97e-a3e1-4743-80bf-29b3bf2c41eb",
+ "workflow_outputs": [
+ {
+ "label": "Uniprot IDs",
+ "output_name": "uniprot_ids",
+ "uuid": "93661860-776f-4cb8-baa7-eda965d2c194"
+ },
+ {
+ "label": "Uniprot IDs",
+ "output_name": "uniprot_ids_csv",
+ "uuid": "a62113ab-6728-48d5-acb4-14bc2bc6795d"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "rpsbml_file": {
+ "id": 1,
+ "output_name": "uniprot_ids"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool BasicDesign",
+ "name": "adv"
+ },
+ {
+ "description": "runtime parameter for tool BasicDesign",
+ "name": "rpsbml_file"
+ }
+ ],
+ "label": null,
+ "name": "BasicDesign",
+ "outputs": [
+ {
+ "name": "sbol_dir",
+ "type": "input"
+ },
+ {
+ "name": "Constructs",
+ "type": "csv"
+ },
+ {
+ "name": "User parts plate",
+ "type": "csv"
+ },
+ {
+ "name": "Biolegio plate",
+ "type": "csv"
+ }
+ ],
+ "position": {
+ "bottom": 583.8000030517578,
+ "height": 214.8000030517578,
+ "left": 386,
+ "right": 586,
+ "top": 369,
+ "width": 200,
+ "x": 386,
+ "y": 369
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+ "tool_shed_repository": {
+ "changeset_revision": "de9f53630349",
+ "name": "rpbasicdesign",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"parts_files\": {\"__class__\": \"RuntimeValue\"}, \"lms_id\": \"LMS\", \"lmp_id\": \"LMP\", \"cds_permutation\": \"true\"}, \"backbone_id\": \"BASIC_SEVA_37_CmR-p15A.1\", \"rpsbml_file\": {\"__class__\": \"RuntimeValue\"}, \"sample_size\": \"88\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "0.3.4",
+ "type": "tool",
+ "uuid": "678a53d3-1241-4f82-8d40-3da99f2be890",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "Biolegio plate",
+ "uuid": "a34be5bd-9da4-461c-bec5-1c4dc5a8c18f"
+ },
+ {
+ "label": null,
+ "output_name": "sbol_dir",
+ "uuid": "469241a2-0ecb-42f5-bcea-53aca636bb46"
+ },
+ {
+ "label": null,
+ "output_name": "Constructs",
+ "uuid": "8755e80f-1ebe-4210-b0df-8acf8218a62c"
+ },
+ {
+ "label": null,
+ "output_name": "User parts plate",
+ "uuid": "ff9e10e0-bfd3-4d0f-98f1-87fd94771293"
+ }
+ ]
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.0.0",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "construct_file": {
+ "id": 2,
+ "output_name": "Constructs"
+ },
+ "plate_files": [
+ {
+ "id": 2,
+ "output_name": "User parts plate"
+ },
+ {
+ "id": 2,
+ "output_name": "Biolegio plate"
+ }
+ ]
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool DNA-Bot",
+ "name": "adv"
+ }
+ ],
+ "label": null,
+ "name": "DNA-Bot",
+ "outputs": [
+ {
+ "name": "dnabot_scripts",
+ "type": "tar"
+ }
+ ],
+ "position": {
+ "bottom": 644.8000030517578,
+ "height": 194.8000030517578,
+ "left": 641.5,
+ "right": 841.5,
+ "top": 450,
+ "width": 200,
+ "x": 641.5,
+ "y": 450
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.0.0",
+ "tool_shed_repository": {
+ "changeset_revision": "6d55c77a17ab",
+ "name": "dnabot",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"default_settings_file\": {\"__class__\": \"RuntimeValue\"}, \"etoh_well\": \"A11\", \"soc_column\": \"1\"}, \"construct_file\": {\"__class__\": \"ConnectedValue\"}, \"plate_files\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "3.0.0",
+ "type": "tool",
+ "uuid": "d5a18d74-8189-48d7-83ca-a63f6f8e1d39",
+ "workflow_outputs": [
+ {
+ "label": "DNA-Bot scripts",
+ "output_name": "dnabot_scripts",
+ "uuid": "e0eabfa3-2dbd-44bc-9471-f8589a1a1861"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "64390e96-9d57-441a-81cf-7544414ea50c",
+ "version": 4
+}
\ No newline at end of file
diff -r 000000000000 -r 7d42adefc60a repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Wed Dec 15 15:59:19 2021 +0000
@@ -0,0 +1,6 @@
+<?xml version="1.0" ?>
+<repositories description="basic assembly workflow">
+ <repository name="selenzy" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="481f7c35323d"/>
+ <repository name="rpbasicdesign" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="de9f53630349"/>
+ <repository name="dnabot" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="6d55c77a17ab"/>
+</repositories>
\ No newline at end of file