Repository 'abrf2017_workshop'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/abrf2017_workshop

Changeset 1:338a6d724774 (2017-03-16)
Previous changeset 0:eb71034189fb (2017-03-02)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
added:
Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga
b
diff -r eb71034189fb -r 338a6d724774 Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga Thu Mar 16 08:45:23 2017 -0400
[
b'@@ -0,0 +1,350 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "ABRF UNIPEPT: Peptide GO Summary Step2", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Gene Ontology Terms"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 193, \n+                "top": 231.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Gene Ontology Terms\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "60bd46b9-2911-4a36-94ac-e51e66a9a6e2", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "7a0ce548-f4a1-4cf9-8e0c-2cc4092eb6cd"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Sample 1 Pept2Prot (extra fields) Normalized"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 195, \n+                "top": 310.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Sample 1 Pept2Prot (extra fields) Normalized\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "52b44ffd-15ff-421b-977a-6b9a512d1582", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "5d5337c5-f228-4054-92cf-f3e800f2a666"\n+                }\n+            ]\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 2, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Sample 1 PSM Report"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 197, \n+                "top": 386.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Sample 1 PSM Report\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "2c906b80-b425-4280-9743-4151b15fd3f4", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "ba24d136-484f-49c8-964f-982b56b26217"\n+                }\n+            ]\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "id": 3, \n+            "input_connections": {\n+                "tables_0|table": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }, \n+                "tables_1|table": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }, \n+                "tables_2|table": {\n+                    "id": 2, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [\n'..b'ool_shed_repository": {\n+                "changeset_revision": "123b9ca5e26a", \n+                "name": "sqlite_to_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"sqlquery\\": \\"\\\\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\\\\\\\\"bering_peptides\\\\\\\\\\\\\\", count(distinct b.id) as \\\\\\\\\\\\\\"bering_psms\\\\\\\\\\\\\\" \\\\\\\\nFROM go as g  JOIN\\\\\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\\\\\n   FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\\\\\n   GROUP BY go.description, bering.peptide, bering_psms.id\\\\\\\\n ) as b ON g.description = b.description \\\\\\\\nWHERE g.aspect = \'cellular_component\'\\\\\\\\nGROUP BY g.description\\\\\\\\nORDER BY  bering_peptides desc,bering_psms desc\\\\\\\\n\\\\\\"\\", \\"__page__\\": 0, \\"sqlitedb\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"false\\\\\\"\\"}", \n+            "tool_version": "0.0.1", \n+            "type": "tool", \n+            "uuid": "4aadf296-0c45-43bb-a146-e267c2955233", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "query_results", \n+                    "uuid": "6042e237-57f6-489e-b8a7-5d32afd39d5e"\n+                }\n+            ]\n+        }, \n+        "6": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", \n+            "id": 6, \n+            "input_connections": {\n+                "sqlitedb": {\n+                    "id": 3, \n+                    "output_name": "sqlitedb"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool SQLite to tabular", \n+                    "name": "sqlitedb"\n+                }\n+            ], \n+            "label": null, \n+            "name": "SQLite to tabular", \n+            "outputs": [\n+                {\n+                    "name": "query_results", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 882, \n+                "top": 458.5\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionquery_results": {\n+                    "action_arguments": {\n+                        "newname": "Bering Strait PEPTIDES and PSMs"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "query_results"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", \n+            "tool_shed_repository": {\n+                "changeset_revision": "123b9ca5e26a", \n+                "name": "sqlite_to_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"sqlquery\\": \\"\\\\\\"SELECT sequence as \\\\\\\\\\\\\\"peptide\\\\\\\\\\\\\\", count(id) as \\\\\\\\\\\\\\"PSMs\\\\\\\\\\\\\\"\\\\\\\\nFROM bering_psms\\\\\\\\nWHERE validation IS NOT \'Confident\' AND confidence >= 95\\\\\\\\nGROUP BY sequence\\\\\\\\nORDER BY sequence\\\\\\\\n\\\\\\"\\", \\"__page__\\": 0, \\"sqlitedb\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"false\\\\\\"\\"}", \n+            "tool_version": "0.0.1", \n+            "type": "tool", \n+            "uuid": "e172020f-dd58-4027-9d6c-94273ec2aee8", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "query_results", \n+                    "uuid": "291d94c5-9ff7-44ae-872f-76955c56d6f4"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "57999e7e-0de6-41e0-87d3-1660414d9896"\n+}\n\\ No newline at end of file\n'