Mercurial > repos > tduigou > retrosynthesis_workflow

changeset 4:807de3ae6160 draft default tip

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 11:10:59 +0000
parents 8766f3348c54
children
files repository_dependencies.xml retrosynthesis_workflow.ga retrosynthesis_workflow/.shed.yml retrosynthesis_workflow/repository_dependencies.xml retrosynthesis_workflow/retrosynthesis_workflow.ga
diffstat 5 files changed, 369 insertions(+), 399 deletions(-) [+]
line wrap: on
line diff
--- /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 @@
+<?xml version="1.0" ?>
+<repositories description="retrosynthesis workflow">
+    <repository name="rrparser" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="392f18980ff4"/>
+    <repository name="rpextractsink" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="dba27c9fb5d6"/>
+    <repository name="retropath2" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="355b5d85c2e8"/>
+    <repository name="rp2paths" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="2c788cd11881"/>
+    <repository name="rpcompletion" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="654f840d108a"/>
+</repositories>
\ No newline at end of file
--- /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
--- 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
--- 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 @@
-<?xml version="1.0" ?>
-<repositories description="retrosynthesis workflow">
-    <repository name="rrparser" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="392f18980ff4"/>
-    <repository name="rpextractsink" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="dba27c9fb5d6"/>
-    <repository name="retropath2" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="355b5d85c2e8"/>
-    <repository name="rp2paths" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="2c788cd11881"/>
-    <repository name="rpcompletion" owner="tduigou" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="6f7feef98f13"/>
-</repositories>
\ No newline at end of file
--- 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"
-                }
-            ],
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