# HG changeset patch
# User tduigou
# Date 1644491459 0
# Node ID 807de3ae61604e9a745a37e159b5dfa157e3b704
# Parent 8766f3348c548b4b5f2faa165c9bc696a179a7aa
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
diff -r 8766f3348c54 -r 807de3ae6160 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Feb 10 11:10:59 2022 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 8766f3348c54 -r 807de3ae6160 retrosynthesis_workflow.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/retrosynthesis_workflow.ga Thu Feb 10 11:10:59 2022 +0000
@@ -0,0 +1,361 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Copy of RetroSynthesis_workflow",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sbml model"
+ }
+ ],
+ "label": "sbml model",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 495.3000030517578,
+ "height": 61.80000305175781,
+ "left": 339,
+ "right": 539,
+ "top": 433.5,
+ "width": 200,
+ "x": 339,
+ "y": 433.5
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "8bb11d3f-e915-4ec1-b9c0-f564ab2e0eee",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "0d8c01b5-de3b-4f6c-816e-f3d50dc39f81"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "RRules Parser",
+ "outputs": [
+ {
+ "name": "out_rules",
+ "type": "csv"
+ }
+ ],
+ "position": {
+ "bottom": 412.6000061035156,
+ "height": 102.60000610351562,
+ "left": 588.5,
+ "right": 788.5,
+ "top": 310,
+ "width": 200,
+ "x": 588.5,
+ "y": 310
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+ "tool_shed_repository": {
+ "changeset_revision": "ea590c609fec",
+ "name": "rrparser",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.4.6",
+ "type": "tool",
+ "uuid": "39cbe6d0-bd77-4b16-9154-39228a68c875",
+ "workflow_outputs": [
+ {
+ "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])",
+ "output_name": "out_rules",
+ "uuid": "2fb329ce-971d-4158-9ec7-9b82c1b39be2"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "InChI of target to produce"
+ }
+ ],
+ "label": "InChI of target to produce",
+ "name": "Input parameter",
+ "outputs": [],
+ "position": {
+ "bottom": 544.1000061035156,
+ "height": 102.60000610351562,
+ "left": 601.5,
+ "right": 801.5,
+ "top": 441.5,
+ "width": 200,
+ "x": 601.5,
+ "y": 441.5
+ },
+ "tool_id": null,
+ "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+ "tool_version": null,
+ "type": "parameter_input",
+ "uuid": "9e4e8764-1433-4bd8-afc0-698fa591ce6d",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "12fa5134-5f52-4ebf-9616-1692e7c2f016"
+ }
+ ]
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "input": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Sink from SBML",
+ "outputs": [
+ {
+ "name": "sink",
+ "type": "csv"
+ }
+ ],
+ "position": {
+ "bottom": 655.1999969482422,
+ "height": 93.19999694824219,
+ "left": 603.5,
+ "right": 803.5,
+ "top": 562,
+ "width": 200,
+ "x": 603.5,
+ "y": 562
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
+ "tool_shed_repository": {
+ "changeset_revision": "47bb93e7832b",
+ "name": "rpextractsink",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"remove_dead_end\": \"true\"}, \"compartment_id\": \"c\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "5.12.1",
+ "type": "tool",
+ "uuid": "65ddba64-bea5-466a-ab26-ba1859009cde",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "sink",
+ "uuid": "c1f1add8-2a31-4849-9aea-312db78d9414"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "rulesfile": {
+ "id": 1,
+ "output_name": "out_rules"
+ },
+ "sinkfile": {
+ "id": 3,
+ "output_name": "sink"
+ },
+ "source_inchi_type|source_inchi": {
+ "id": 2,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "RetroPath2.0",
+ "outputs": [
+ {
+ "name": "Reaction_Network",
+ "type": "csv"
+ }
+ ],
+ "position": {
+ "bottom": 569,
+ "height": 154,
+ "left": 900.5,
+ "right": 1100.5,
+ "top": 415,
+ "width": 200,
+ "x": 900.5,
+ "y": 415
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
+ "tool_shed_repository": {
+ "changeset_revision": "9c8ac9980bd6",
+ "name": "retropath2",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"version\": \"r20220104\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"timeout\": \"60\"}, \"max_steps\": \"3\", \"rulesfile\": {\"__class__\": \"ConnectedValue\"}, \"sinkfile\": {\"__class__\": \"ConnectedValue\"}, \"source_inchi_type\": {\"inchi_type\": \"string\", \"__current_case__\": 0, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.0",
+ "type": "tool",
+ "uuid": "7dd663f6-6633-41f0-b9cd-4bf575f72b90",
+ "workflow_outputs": [
+ {
+ "label": "RetroPath2.0",
+ "output_name": "Reaction_Network",
+ "uuid": "48e8b7d2-f341-4cff-b410-30652e68dab4"
+ }
+ ]
+ },
+ "5": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3",
+ "errors": null,
+ "id": 5,
+ "input_connections": {
+ "rp2_pathways": {
+ "id": 4,
+ "output_name": "Reaction_Network"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "RP2paths",
+ "outputs": [
+ {
+ "name": "master_pathways",
+ "type": "csv"
+ },
+ {
+ "name": "compounds",
+ "type": "tsv"
+ }
+ ],
+ "position": {
+ "bottom": 526.3999938964844,
+ "height": 164.39999389648438,
+ "left": 1193.5,
+ "right": 1393.5,
+ "top": 362,
+ "width": 200,
+ "x": 1193.5,
+ "y": 362
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3",
+ "tool_shed_repository": {
+ "changeset_revision": "2782bee7c5a6",
+ "name": "rp2paths",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "1.4.3",
+ "type": "tool",
+ "uuid": "0d9f290f-a11c-4471-ba16-e0c561634be5",
+ "workflow_outputs": [
+ {
+ "label": "RP2paths (Pathways)",
+ "output_name": "master_pathways",
+ "uuid": "2225e9b3-8984-4d53-9878-232b4f773869"
+ },
+ {
+ "label": "RP2paths (Compounds)",
+ "output_name": "compounds",
+ "uuid": "651afa73-ad92-4296-b788-00bd78f6df32"
+ }
+ ]
+ },
+ "6": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1",
+ "errors": null,
+ "id": 6,
+ "input_connections": {
+ "rp2_pathways": {
+ "id": 4,
+ "output_name": "Reaction_Network"
+ },
+ "rp2paths_compounds": {
+ "id": 5,
+ "output_name": "compounds"
+ },
+ "rp2paths_pathways": {
+ "id": 5,
+ "output_name": "master_pathways"
+ },
+ "sink": {
+ "id": 3,
+ "output_name": "sink"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Complete Reactions",
+ "outputs": [
+ {
+ "name": "pathways",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "bottom": 807.6000061035156,
+ "height": 245.60000610351562,
+ "left": 1447.5,
+ "right": 1647.5,
+ "top": 562,
+ "width": 200,
+ "x": 1447.5,
+ "y": 562
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1",
+ "tool_shed_repository": {
+ "changeset_revision": "b8242cf18cc0",
+ "name": "rpcompletion",
+ "owner": "tduigou",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": {\"max_subpaths_filter\": \"10\", \"upper_flux_bound\": \"999999\", \"lower_flux_bound\": \"0\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_compounds\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_pathways\": {\"__class__\": \"ConnectedValue\"}, \"sink\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "5.12.1",
+ "type": "tool",
+ "uuid": "9acba2e0-e30c-47a7-8166-a6d694e425f8",
+ "workflow_outputs": [
+ {
+ "label": "Complete Reactions",
+ "output_name": "pathways",
+ "uuid": "fd9a697a-6bf9-4b84-88bf-a1c749475e30"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "c563c2dc-6f52-45c3-978a-43777561081d",
+ "version": 9
+}
\ No newline at end of file
diff -r 8766f3348c54 -r 807de3ae6160 retrosynthesis_workflow/.shed.yml
--- a/retrosynthesis_workflow/.shed.yml Wed Feb 09 15:35:38 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-categories:
-- Synthetic Biology
-description: Workflow to process Retrosynthesis and Pathway Enumeration
-homepage_url: ''
-long_description: "The workflow generates theoretical possible pathways for the production\
- \ of a target molecule in an organism of choice. Three key steps are performed in\
- \ this workflow. First, using the RetroPath2.0 node, it generates feasible metabolic\
- \ routes between a collection of chemical species contained within a GEM SBML file\
- \ of the selected organism, a target molecule that the user wishes to produce, and\
- \ reaction rules extracted from RetroRules. That metabolic network is then deconstructed\
- \ into individual pathways using the RP2paths node. Lastly, those individual metabolic\
- \ pathways are converted to SBML files using \u201CComplete Reactions\u201D node.\
- \ The former generates SBML files describing the individual heterologous pathways\
- \ while the latter adds the appropriate cofactors and removes duplicate pathways.\
- \ Source codes may be found at the following locations: https://github.com/brsynth/synbiocad-galaxy-wrappers/tree/master/RRulesParser\
- \ , https://github.com/galaxy-synbiocad/galaxy-nodes/tree/master/rpExtractSink ,\
- \ https://github.com/galaxy-synbiocad/galaxy-nodes/tree/master/RetroPath2-wrapper\
- \ , https://github.com/galaxy-synbiocad/galaxy-nodes/tree/master/rp2paths , https://github.com/brsynth/synbiocad-galaxy-wrappers/tree/master/rpCompletion\
- \ ."
-name: retrosynthesis_workflow
-owner: tduigou
diff -r 8766f3348c54 -r 807de3ae6160 retrosynthesis_workflow/repository_dependencies.xml
--- a/retrosynthesis_workflow/repository_dependencies.xml Wed Feb 09 15:35:38 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-
-
-
-
-
-
-
-
\ No newline at end of file
diff -r 8766f3348c54 -r 807de3ae6160 retrosynthesis_workflow/retrosynthesis_workflow.ga
--- a/retrosynthesis_workflow/retrosynthesis_workflow.ga Wed Feb 09 15:35:38 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,370 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "",
- "format-version": "0.1",
- "name": "RetroSynthesis_workflow",
- "steps": {
- "0": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 0,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "sbml model"
- }
- ],
- "label": "sbml model",
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "bottom": 335.3000030517578,
- "height": 61.80000305175781,
- "left": 278.5,
- "right": 478.5,
- "top": 273.5,
- "width": 200,
- "x": 278.5,
- "y": 273.5
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
- "type": "data_input",
- "uuid": "8bb11d3f-e915-4ec1-b9c0-f564ab2e0eee",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "1fa2a565-bbb4-4817-a142-cb6614aeba85"
- }
- ]
- },
- "1": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5",
- "errors": null,
- "id": 1,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "RRules Parser",
- "outputs": [
- {
- "name": "out_rules",
- "type": "csv"
- }
- ],
- "position": {
- "bottom": 281.1000061035156,
- "height": 102.60000610351562,
- "left": 530.5,
- "right": 730.5,
- "top": 178.5,
- "width": 200,
- "x": 530.5,
- "y": 178.5
- },
- "post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5",
- "tool_shed_repository": {
- "changeset_revision": "024dcd6421db",
- "name": "rrparser",
- "owner": "tduigou",
- "tool_shed": "toolshed.g2.bx.psu.edu"
- },
- "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 2}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": null,
- "type": "tool",
- "uuid": "e7a835df-5172-4fdf-a2a3-81c41a73bc00",
- "workflow_outputs": [
- {
- "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])",
- "output_name": "out_rules",
- "uuid": "938b8abf-ce03-476e-b92a-39dd14cbd643"
- }
- ]
- },
- "2": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 2,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "InChI of target to produce"
- }
- ],
- "label": "InChI of target to produce",
- "name": "Input parameter",
- "outputs": [],
- "position": {
- "bottom": 440.6999969482422,
- "height": 82.19999694824219,
- "left": 518,
- "right": 718,
- "top": 358.5,
- "width": 200,
- "x": 518,
- "y": 358.5
- },
- "tool_id": null,
- "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
- "tool_version": null,
- "type": "parameter_input",
- "uuid": "95271805-5e3f-40d4-b262-f162cbb790eb",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "ce569b93-19c3-4ea7-bbeb-824d8416bd80"
- }
- ]
- },
- "3": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2",
- "errors": null,
- "id": 3,
- "input_connections": {
- "input": {
- "id": 0,
- "output_name": "output"
- }
- },
- "inputs": [],
- "label": null,
- "name": "Sink from SBML",
- "outputs": [
- {
- "name": "sink",
- "type": "csv"
- }
- ],
- "position": {
- "bottom": 570.6999969482422,
- "height": 93.19999694824219,
- "left": 516.5,
- "right": 716.5,
- "top": 477.5,
- "width": 200,
- "x": 516.5,
- "y": 477.5
- },
- "post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2",
- "tool_shed_repository": {
- "changeset_revision": "f664f3c3aca8",
- "name": "rpextractsink",
- "owner": "tduigou",
- "tool_shed": "toolshed.g2.bx.psu.edu"
- },
- "tool_state": "{\"adv\": {\"compartment_id\": \"MNXC3\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"remove_dead_end\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": null,
- "type": "tool",
- "uuid": "b8c49635-e74d-41d6-b1ee-7881087039c9",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "sink",
- "uuid": "9398d924-57ce-4b29-924c-db2baec7f913"
- }
- ]
- },
- "4": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4",
- "errors": null,
- "id": 4,
- "input_connections": {
- "rulesfile": {
- "id": 1,
- "output_name": "out_rules"
- },
- "sinkfile": {
- "id": 3,
- "output_name": "sink"
- },
- "source_inchi": {
- "id": 2,
- "output_name": "output"
- }
- },
- "inputs": [
- {
- "description": "runtime parameter for tool RetroPath2.0",
- "name": "rulesfile"
- },
- {
- "description": "runtime parameter for tool RetroPath2.0",
- "name": "sinkfile"
- }
- ],
- "label": null,
- "name": "RetroPath2.0",
- "outputs": [
- {
- "name": "Reaction_Network",
- "type": "csv"
- }
- ],
- "position": {
- "bottom": 504.5,
- "height": 154,
- "left": 794.5,
- "right": 994.5,
- "top": 350.5,
- "width": 200,
- "x": 794.5,
- "y": 350.5
- },
- "post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4",
- "tool_shed_repository": {
- "changeset_revision": "6cdbb534cbca",
- "name": "retropath2",
- "owner": "tduigou",
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