Mercurial > repos > tduigou > pathway_analysis_workflow

changeset 0:8fb4e270be9f draft default tip

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 19:02:39 +0000
parents
children
files Pathway_Analysis_workflow.ga repository_dependencies.xml
diffstat 2 files changed, 304 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Pathway_Analysis_workflow.ga	Mon Dec 13 19:02:39 2021 +0000
@@ -0,0 +1,296 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "format-version": "0.1",
+    "name": "Pathway_Analysis_workflow",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "rpbsml_pathways"
+                }
+            ],
+            "label": "rpbsml_pathways",
+            "name": "Input dataset collection",
+            "outputs": [],
+            "position": {
+                "bottom": 522.8000030517578,
+                "height": 61.80000305175781,
+                "left": -138,
+                "right": 62,
+                "top": 461,
+                "width": 200,
+                "x": -138,
+                "y": 461
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+            "tool_version": null,
+            "type": "data_collection_input",
+            "uuid": "40022f70-14b3-4291-aa3b-8f2693d6752c",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "760719ed-d2e1-47d5-9f46-d6dd876f6b6c"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "sbml_model"
+                }
+            ],
+            "label": "sbml_model",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 632.8000030517578,
+                "height": 61.80000305175781,
+                "left": -137,
+                "right": 63,
+                "top": 571,
+                "width": 200,
+                "x": -137,
+                "y": 571
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "715f8537-ff4b-4b00-86a2-0c358576ddd8",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "80fd34b8-0b64-4bd7-8860-4354ecc86f78"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpfba/rpFBA/5.9.2",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "model": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "FBA",
+            "outputs": [
+                {
+                    "name": "pathway_with_fba",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 612.6000061035156,
+                "height": 123.60000610351562,
+                "left": 157,
+                "right": 357,
+                "top": 489,
+                "width": 200,
+                "x": 157,
+                "y": 489
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpfba/rpFBA/5.9.2",
+            "tool_shed_repository": {
+                "changeset_revision": "fb5efc456dcc",
+                "name": "rpfba",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"merge\": \"false\", \"ignore_orphan_species\": \"true\", \"log_level\": \"error\"}, \"compartment_id\": \"MNXC3\", \"input_sim_type\": {\"sim_type\": \"fraction\", \"__current_case__\": 0, \"fraction_of\": \"0.75\", \"objective_rxn_id\": \"rxn_target\", \"biomass_rxn_id\": \"biomass\"}, \"model\": {\"__class__\": \"ConnectedValue\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.9.2",
+            "type": "tool",
+            "uuid": "219ff424-7956-43bc-adaf-ebbb4341af01",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "pathway_with_fba",
+                    "uuid": "91b6f335-54fa-42bd-a6bb-2ff71f2fd50b"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpThermo/5.9.2",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "input": {
+                    "id": 2,
+                    "output_name": "pathway_with_fba"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Thermodynamics",
+            "outputs": [
+                {
+                    "name": "pathway_with_thermo",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 604.6000061035156,
+                "height": 113.60000610351562,
+                "left": 439,
+                "right": 639,
+                "top": 491,
+                "width": 200,
+                "x": 439,
+                "y": 491
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpThermo/5.9.2",
+            "tool_shed_repository": {
+                "changeset_revision": "44e54b56328d",
+                "name": "rpthermo",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"ph\": \"7.5\", \"ionic_strength\": \"200.0\", \"pMg\": \"10.0\", \"temp_k\": \"298.15\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.9.2",
+            "type": "tool",
+            "uuid": "24b0f086-293c-45cf-be0e-b17265316a38",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "pathway_with_thermo",
+                    "uuid": "f0c3c790-65ac-42d9-8793-9ec26327ad74"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.9.2",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "pathway": {
+                    "id": 3,
+                    "output_name": "pathway_with_thermo"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Score Pathway",
+            "outputs": [
+                {
+                    "name": "scored_pathway",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 604.1999969482422,
+                "height": 93.19999694824219,
+                "left": 692,
+                "right": 892,
+                "top": 511,
+                "width": 200,
+                "x": 692,
+                "y": 511
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.9.2",
+            "tool_shed_repository": {
+                "changeset_revision": "f818d489ca7d",
+                "name": "rpscore",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"no_of_rxns_thres\": \"10\", \"log_level\": \"error\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.9.2",
+            "type": "tool",
+            "uuid": "418f937f-5114-4330-9825-42a2c0028b78",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "scored_pathway",
+                    "uuid": "c99d61ef-cd94-48be-ae0e-fbac6c6b5d5b"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.10.0",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "pathway_collection": {
+                    "id": 4,
+                    "output_name": "scored_pathway"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Rank Pathways",
+                    "name": "pathway_collection"
+                }
+            ],
+            "label": null,
+            "name": "Rank Pathways",
+            "outputs": [
+                {
+                    "name": "sorted_pathways",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 635.1999969482422,
+                "height": 93.19999694824219,
+                "left": 933,
+                "right": 1133,
+                "top": 542,
+                "width": 200,
+                "x": 933,
+                "y": 542
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.10.0",
+            "tool_shed_repository": {
+                "changeset_revision": "e95370d2e5f9",
+                "name": "rpranker",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"pathway_collection\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.10.0",
+            "type": "tool",
+            "uuid": "2035ac50-9127-4363-90f5-86990ecc4239",
+            "workflow_outputs": [
+                {
+                    "label": "Ranked Pathways",
+                    "output_name": "sorted_pathways",
+                    "uuid": "db1ad6c3-983a-4678-8db0-fe5c59b81025"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "f1092980-8652-4560-bda2-ed95629cad24",
+    "version": 3
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Dec 13 19:02:39 2021 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0" ?>
+<repositories description="pathway analysis workflow">
+    <repository name="rpfba" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="fb5efc456dcc"/>
+    <repository name="rpthermo" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="44e54b56328d"/>
+    <repository name="rpscore" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="f818d489ca7d"/>
+    <repository name="rpranker" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="e95370d2e5f9"/>
+    <repository name="rpcompletion" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="98d925a75257"/>
+</repositories>
\ No newline at end of file