Mercurial > repos > tduigou > retrosynthesis_workflow

changeset 0:5aa8c015b750 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 02 Dec 2021 14:11:13 +0000
parents
children e5803ef59eb6
files repository_dependencies.xml retrosynthesis_workflow.ga
diffstat 2 files changed, 378 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Dec 02 14:11:13 2021 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0" ?>
+<repositories description="retrosynthesis workflow">
+    <repository changeset_revision="024dcd6421db" name="rrparser" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="f664f3c3aca8" name="rpextractsink" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="6cdbb534cbca" name="retropath2" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="2782bee7c5a6" name="rp2paths" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="98d925a75257" name="rpcompletion" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/retrosynthesis_workflow.ga	Thu Dec 02 14:11:13 2021 +0000
@@ -0,0 +1,370 @@
+{
+    "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",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"max_steps\": \"3\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"mwmax_cof\": \"1000\", \"timeout\": \"60\"}, \"rulesfile\": {\"__class__\": \"RuntimeValue\"}, \"sinkfile\": {\"__class__\": \"RuntimeValue\"}, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": null,
+            "type": "tool",
+            "uuid": "e705e614-950a-436a-96a8-f8e9bcc4bb64",
+            "workflow_outputs": [
+                {
+                    "label": "RetroPath2.0",
+                    "output_name": "Reaction_Network",
+                    "uuid": "31cac3f6-2f12-48c4-b265-9d745d5ba36d"
+                }
+            ]
+        },
+        "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": 437.8999938964844,
+                "height": 164.39999389648438,
+                "left": 1050.5,
+                "right": 1250.5,
+                "top": 273.5,
+                "width": 200,
+                "x": 1050.5,
+                "y": 273.5
+            },
+            "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": null,
+            "type": "tool",
+            "uuid": "3ebbcfa4-dd81-4200-b023-dbb445131657",
+            "workflow_outputs": [
+                {
+                    "label": "RP2paths (Pathways)",
+                    "output_name": "master_pathways",
+                    "uuid": "9b5454c6-35e7-4632-96d3-2d75ba8b1afe"
+                },
+                {
+                    "label": "RP2paths (Compounds)",
+                    "output_name": "compounds",
+                    "uuid": "fc35e5fb-8556-4c7f-b11f-45b93467f7f6"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2",
+            "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": 646.1000061035156,
+                "height": 245.60000610351562,
+                "left": 1323.5,
+                "right": 1523.5,
+                "top": 400.5,
+                "width": 200,
+                "x": 1323.5,
+                "y": 400.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2",
+            "tool_shed_repository": {
+                "changeset_revision": "98d925a75257",
+                "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": null,
+            "type": "tool",
+            "uuid": "bfc32617-1870-4240-8cf6-ea93da840007",
+            "workflow_outputs": [
+                {
+                    "label": "Complete Reactions",
+                    "output_name": "pathways",
+                    "uuid": "b77df22c-2b09-4787-8762-18f3fd748aea"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "a8283850-4dcb-4bd9-a11e-507bf58e8b4b",
+    "version": 8
+}
\ No newline at end of file