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

Changeset 0:eb71034189fb (2017-03-02)
Next changeset 1:338a6d724774 (2017-03-16)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
added:
Galaxy-Workflow-ABRF_2017_Taxonomy_Comparison_Workflow.ga
Galaxy-Workflow-ABRF_2017_Workflow_for_Functional_Comparison.ga
Galaxy-Workflow-ABRF_UNIPEPT_Taxonomy_Workflow_Bering_Strait.ga
Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Annotation_Step1.ga
repository_dependencies.xml
b
diff -r 000000000000 -r eb71034189fb Galaxy-Workflow-ABRF_2017_Taxonomy_Comparison_Workflow.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-ABRF_2017_Taxonomy_Comparison_Workflow.ga Thu Mar 02 15:42:24 2017 -0500
[
b'@@ -0,0 +1,437 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "ABRF 2017:Taxonomy Comparison Workflow", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "PSM Report (Bering Strait)"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 296, \n+                "top": 186\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"PSM Report (Bering Strait)\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "c404eaed-7c90-4b48-82c4-9083bdb6db29", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "0bfee776-11e1-4553-a7ee-25fd0c628891"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "PSM Report (Chukchi Sea)"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 352, \n+                "top": 596.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"PSM Report (Chukchi Sea)\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "c6e42b4c-4116-48eb-92a2-bebdbceaba1d", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "0d4f355a-1f05-49a9-a5a3-2f58fc25ca32"\n+                }\n+            ]\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "id": 2, \n+            "input_connections": {\n+                "tables_0|table": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool Query Tabular", \n+                    "name": "add_to_database"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Query Tabular", \n+            "outputs": [\n+                {\n+                    "name": "sqlitedb", \n+                    "type": "sqlite"\n+                }, \n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 453, \n+                "top": 335\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionsqlitedb": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "sqlitedb"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "tool_shed_repository": {\n+                "changeset_revision": "e84d1c3bf4fe", \n+                "name": "query_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"tables\\": \\"[{\\'..b' \\\\\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 0, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"include_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"^\\\\\\\\\\\\\\\\d\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}, {\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"bering_lca\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"peptide,,,,,,,,,,,,,,,,,,,,,genus\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 1, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"comment_char\\\\\\": \\\\\\"#\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"filter_type\\\\\\": \\\\\\"comment\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}, {\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"chukchi_psm\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 2, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"include_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"^\\\\\\\\\\\\\\\\d\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}, {\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"chukchi_lca\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"peptide,,,,,,,,,,,,,,,,,,,,,genus\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 3, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"comment_char\\\\\\": \\\\\\"#\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"filter_type\\\\\\": \\\\\\"comment\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}]\\", \\"save_db\\": \\"\\\\\\"true\\\\\\"\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"false\\\\\\"\\", \\"sqlquery\\": \\"\\\\\\"SELECT taxon.genus, bering.psms as \\\\\\\\\\\\\\"BeringStrait_PSMs\\\\\\\\\\\\\\", chukchi.psms as \\\\\\\\\\\\\\"ChukchiSea_PSMs\\\\\\\\\\\\\\",\\\\\\\\nbering.peptides as \\\\\\\\\\\\\\"BeringStrait_Peptides\\\\\\\\\\\\\\", chukchi.peptides as \\\\\\\\\\\\\\"ChukchiSea_Peptides\\\\\\\\\\\\\\"\\\\\\\\nFROM\\\\\\\\n (SELECT distinct genus FROM bering_lca WHERE genus IS NOT NULL\\\\\\\\n  UNION\\\\\\\\n  SELECT distinct genus FROM chukchi_lca WHERE genus IS NOT NULL) as taxon\\\\\\\\n LEFT OUTER JOIN\\\\\\\\n (SELECT bering_lca.genus,count(bering_psm.sequence) as \\\\\\\\\\\\\\"psms\\\\\\\\\\\\\\",count(distinct bering_psm.sequence) as \\\\\\\\\\\\\\"peptides\\\\\\\\\\\\\\"\\\\\\\\n  FROM bering_psm LEFT JOIN bering_lca ON bering_psm.sequence = bering_lca.peptide\\\\\\\\n  WHERE validation IS NOT \'Confident\'\\\\\\\\n  AND confidence >= 95\\\\\\\\n  GROUP BY bering_lca.genus ) as bering\\\\\\\\n ON taxon.genus = bering.genus\\\\\\\\n LEFT OUTER JOIN\\\\\\\\n (SELECT chukchi_lca.genus,count(chukchi_psm.sequence) as \\\\\\\\\\\\\\"psms\\\\\\\\\\\\\\",count(distinct chukchi_psm.sequence) as \\\\\\\\\\\\\\"peptides\\\\\\\\\\\\\\"\\\\\\\\n  FROM chukchi_psm LEFT JOIN chukchi_lca ON chukchi_psm.sequence = chukchi_lca.peptide\\\\\\\\n  WHERE validation IS NOT \'Confident\'\\\\\\\\n  AND confidence >= 95\\\\\\\\n  GROUP BY chukchi_lca.genus) as chukchi\\\\\\\\n ON taxon.genus = chukchi.genus\\\\\\\\nWHERE bering.psms IS NOT NULL OR chukchi.psms IS NOT NULL\\\\\\\\nORDER BY taxon.genus\\\\\\\\n\\\\\\"\\", \\"add_to_database\\": \\"{\\\\\\"withdb\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}\\", \\"workdb\\": \\"\\\\\\"workdb.sqlite\\\\\\"\\"}", \n+            "tool_version": "2.0.0", \n+            "type": "tool", \n+            "uuid": "c8b14d06-f3a3-46db-b3c6-01f5c50bc16e", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "ea8853c6-d1e2-4c04-a795-4b1af5e50ff4"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "8fac309b-4ea6-4c20-9e40-651b2346b3e8"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r eb71034189fb Galaxy-Workflow-ABRF_2017_Workflow_for_Functional_Comparison.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-ABRF_2017_Workflow_for_Functional_Comparison.ga Thu Mar 02 15:42:24 2017 -0500
[
b'@@ -0,0 +1,422 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "ABRF 2017 Workflow for Functional Comparison", \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": 177, \n+                "top": 188.5\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": "6f5a7554-d201-4f17-8e47-8e07ead87e52", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "1e545169-c1d0-4da0-9f5d-09632dffbd6a"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Bering Strait Pept2Prot (extra fields) Normalized"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 181, \n+                "top": 264.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Bering Strait Pept2Prot (extra fields) Normalized\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "caae62e0-46f1-4f84-934f-31be41856bb0", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "27ccf52d-44c0-43eb-bf66-bee437cfbcfa"\n+                }\n+            ]\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 2, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Chukchi Sea Pept2Prot (extra fields) Normalized"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 185, \n+                "top": 354.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Chukchi Sea Pept2Prot (extra fields) Normalized\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "3c954f78-1ef3-4cae-bb4e-c768d9904506", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "67cf7d09-93cf-4e90-9f2c-1f9c61973cff"\n+                }\n+            ]\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 3, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Bering Strait PSM Report"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 187, \n+                "top": 442.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id"'..b'ering.peptide, bering_psms.id\\\\\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\\\\\n   FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\\\\\n   GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\\\\\n ) as c ON g.description = c.description\\\\\\\\nWHERE g.aspect = \'cellular_component\'\\\\\\\\nGROUP BY g.description\\\\\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\\\\"\\", \\"__page__\\": 0, \\"sqlitedb\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"false\\\\\\"\\"}", \n+            "tool_version": "0.0.1", \n+            "type": "tool", \n+            "uuid": "d0f27344-2721-47e3-891a-0a9288293945", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "query_results", \n+                    "uuid": "80f8307d-68d7-4a49-bae8-b43957dd3098"\n+                }\n+            ]\n+        }, \n+        "8": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", \n+            "id": 8, \n+            "input_connections": {\n+                "sqlitedb": {\n+                    "id": 5, \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": 883, \n+                "top": 457.5\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionquery_results": {\n+                    "action_arguments": {\n+                        "newname": "PEPTIDE PSM COUNTS COMPARISON"\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": "78e9570fbe08", \n+                "name": "sqlite_to_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"sqlquery\\": \\"\\\\\\"SELECT peptides.peptide, count(bering_psms.id)*1.42 as \\\\\\\\\\\\\\"BeringStrait_PSMs\\\\\\\\\\\\\\", count(chukchi_psms.id) as \\\\\\\\\\\\\\"ChukchiSea_PSMs\\\\\\\\\\\\\\"\\\\\\\\nFROM \\\\\\\\n(SELECT distinct sequence \\\\\\\\\\\\\\"peptide\\\\\\\\\\\\\\" FROM bering_psms UNION SELECT sequence as \\\\\\\\\\\\\\"peptide\\\\\\\\\\\\\\" FROM chukchi_psms) as peptides\\\\\\\\nLEFT JOIN bering_psms ON peptides.peptide = bering_psms.sequence\\\\\\\\nLEFT JOIN chukchi_psms ON peptides.peptide = chukchi_psms.sequence\\\\\\\\nGROUP BY peptides.peptide\\\\\\\\nORDER BY peptides.peptide\\\\\\\\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": "a3b80420-6655-4acf-b62b-dcb4ac5d9c6e", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "query_results", \n+                    "uuid": "a9b9c19b-8ab2-4f08-9c1f-73e6991f58f9"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "9f54fdad-4b9b-4389-8c3a-4512f0cf8df5"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r eb71034189fb Galaxy-Workflow-ABRF_UNIPEPT_Taxonomy_Workflow_Bering_Strait.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-ABRF_UNIPEPT_Taxonomy_Workflow_Bering_Strait.ga Thu Mar 02 15:42:24 2017 -0500
[
b'@@ -0,0 +1,311 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "ABRF UNIPEPT:Taxonomy Workflow Bering Strait", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "PSM Report"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 189, \n+                "top": 163\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"PSM Report\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "22470252-89e0-47c6-ba28-5efab1803316", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "8c57d953-0eca-4d62-8e5c-2ad994f7db4b"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "id": 1, \n+            "input_connections": {\n+                "tables_0|table": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool Query Tabular", \n+                    "name": "add_to_database"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Query Tabular", \n+            "outputs": [\n+                {\n+                    "name": "sqlitedb", \n+                    "type": "sqlite"\n+                }, \n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 397, \n+                "top": 295\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionsqlitedb": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "sqlitedb"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "tool_shed_repository": {\n+                "changeset_revision": "ae27dab228b8", \n+                "name": "query_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"tables\\": \\"[{\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"psm\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 0, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"include_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"^\\\\\\\\\\\\\\\\d\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}]\\", \\"save_db\\": \\"\\\\\\"true\\\\\\"\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"true\\\\\\"\\", \\"sqlquery\\": \\"\\\\\\"SELECT distinct sequence \\\\\\\\nFROM psm \\\\\\\\nWHERE validation IS NOT \'Confident\' AND confidence >= 95 \\\\\\\\nORDER BY sequence\\\\\\"\\", \\"add_to_database\\": \\"{\\\\\\"withdb\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}\\", \\"workdb\\": \\"\\\\\\"workdb.sqlite\\\\\\"\\"}", \n+            "tool_version": "2.0.0", \n+            "type": "tool", \n+            "uuid": "b210efa3-4926-4e07-99e6-2619258d28a'..b'              "tables_1|table": {\n+                    "id": 3, \n+                    "output_name": "output_tsv"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool Query Tabular", \n+                    "name": "add_to_database"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Query Tabular", \n+            "outputs": [\n+                {\n+                    "name": "sqlitedb", \n+                    "type": "sqlite"\n+                }, \n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 1044, \n+                "top": 162\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionsqlitedb": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "sqlitedb"\n+                }, \n+                "RenameDatasetActionoutput": {\n+                    "action_arguments": {\n+                        "newname": "Unipept: TAXONOMY GENUS PSMs Peptides (Bering Strait)"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "output"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "tool_shed_repository": {\n+                "changeset_revision": "ae27dab228b8", \n+                "name": "query_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"tables\\": \\"[{\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"psm\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 0, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"include_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"^\\\\\\\\\\\\\\\\d\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}, {\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"lca\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"peptide,,,,,,,,,,,,,,,,,,,,,genus\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 1, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"exclude_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"#peptide\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}]\\", \\"save_db\\": \\"\\\\\\"false\\\\\\"\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"false\\\\\\"\\", \\"sqlquery\\": \\"\\\\\\"SELECT lca.genus,count(psm.sequence) as \\\\\\\\\\\\\\"PSMs\\\\\\\\\\\\\\",count(distinct psm.sequence) as \\\\\\\\\\\\\\"DISTINCT PEPTIDES\\\\\\\\\\\\\\" \\\\\\\\nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \\\\\\\\nWHERE validation IS NOT \'Confident\' \\\\\\\\nAND confidence >= 95 \\\\\\\\nGROUP BY lca.genus \\\\\\\\nORDER BY PSMs desc, \'DISTINCT PEPTIDES\' desc\\\\\\"\\", \\"add_to_database\\": \\"{\\\\\\"withdb\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}\\", \\"workdb\\": \\"\\\\\\"workdb.sqlite\\\\\\"\\"}", \n+            "tool_version": "2.0.0", \n+            "type": "tool", \n+            "uuid": "4ac60e8a-cc65-48c8-9ea5-a26b35b90558", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "c618c51e-2f1e-437c-a570-981d2d07ea02"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "87aed6af-eb3b-4d42-99c0-e1a62fd59413"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r eb71034189fb Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Annotation_Step1.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Annotation_Step1.ga Thu Mar 02 15:42:24 2017 -0500
[
b'@@ -0,0 +1,226 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "ABRF UNIPEPT: Peptide GO Annotation Step1", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "PSM Report"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 204, \n+                "top": 200\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"PSM Report\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "19976c04-5769-48c8-a26f-931d821db5df", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "62d54f79-3123-4816-98c8-2746e1570ec3"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "id": 1, \n+            "input_connections": {\n+                "tables_0|table": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool Query Tabular", \n+                    "name": "add_to_database"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Query Tabular", \n+            "outputs": [\n+                {\n+                    "name": "sqlitedb", \n+                    "type": "sqlite"\n+                }, \n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 432, \n+                "top": 203\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionsqlitedb": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "sqlitedb"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", \n+            "tool_shed_repository": {\n+                "changeset_revision": "ae27dab228b8", \n+                "name": "query_tabular", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"tables\\": \\"[{\\\\\\"tbl_opts\\\\\\": {\\\\\\"load_named_columns\\\\\\": \\\\\\"true\\\\\\", \\\\\\"pkey_autoincr\\\\\\": \\\\\\"\\\\\\", \\\\\\"table_name\\\\\\": \\\\\\"psm\\\\\\", \\\\\\"col_names\\\\\\": \\\\\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\\\\", \\\\\\"indexes\\\\\\": []}, \\\\\\"__index__\\\\\\": 0, \\\\\\"input_opts\\\\\\": {\\\\\\"linefilters\\\\\\": [{\\\\\\"filter\\\\\\": {\\\\\\"regex_action\\\\\\": \\\\\\"include_match\\\\\\", \\\\\\"regex_pattern\\\\\\": \\\\\\"^\\\\\\\\\\\\\\\\d\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"filter_type\\\\\\": \\\\\\"regex\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]}, \\\\\\"table\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}]\\", \\"save_db\\": \\"\\\\\\"true\\\\\\"\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"no_header\\": \\"\\\\\\"true\\\\\\"\\", \\"sqlquery\\": \\"\\\\\\"SELECT distinct sequence \\\\\\\\nFROM psm \\\\\\\\nWHERE validation IS NOT \'Confident\' AND confidence >= 95 \\\\\\\\nORDER BY sequence\\\\\\"\\", \\"add_to_database\\": \\"{\\\\\\"withdb\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}\\", \\"workdb\\": \\"\\\\\\"workdb.sqlite\\\\\\"\\"}", \n+            "tool_version": "2.0.0", \n+            "type": "tool", \n+            "uuid": "a8789ea6-f25f-4f27-b687-351356e81967",'..b'          }, \n+            "post_job_actions": {\n+                "HideDatasetActionoutput_csv": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_csv"\n+                }, \n+                "HideDatasetActionoutput_json": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_json"\n+                }, \n+                "HideDatasetActionoutput_unmatched": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_unmatched"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", \n+            "tool_shed_repository": {\n+                "changeset_revision": "34758ab8aaa4", \n+                "name": "unipept", \n+                "owner": "galaxyp", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"__page__\\": 0, \\"outputs\\": \\"[\\\\\\"tsv\\\\\\"]\\", \\"__rerun_remap_job_id__\\": null, \\"peptide_src\\": \\"{\\\\\\"column\\\\\\": \\\\\\"1\\\\\\", \\\\\\"fmt\\\\\\": \\\\\\"tabular\\\\\\", \\\\\\"input_tsv\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"__current_case__\\\\\\": 1}\\", \\"strict\\": \\"\\\\\\"false\\\\\\"\\", \\"unipept\\": \\"{\\\\\\"api\\\\\\": \\\\\\"pept2prot\\\\\\", \\\\\\"equate_il\\\\\\": \\\\\\"true\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"extra\\\\\\": \\\\\\"true\\\\\\"}\\"}", \n+            "tool_version": "2.0.1", \n+            "type": "tool", \n+            "uuid": "cf10a931-a775-441b-a8d7-6e03e45fa9db", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output_tsv", \n+                    "uuid": "243231a1-d987-4331-ad40-d5f6c92bc828"\n+                }\n+            ]\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/split_tabular_columns/split_tabular_columns/0.0.1", \n+            "id": 3, \n+            "input_connections": {\n+                "input": {\n+                    "id": 2, \n+                    "output_name": "output_tsv"\n+                }\n+            }, \n+            "inputs": [\n+                {\n+                    "description": "runtime parameter for tool Split Tabular Columns", \n+                    "name": "input"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Split Tabular Columns", \n+            "outputs": [\n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 1051, \n+                "top": 200.5\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/split_tabular_columns/split_tabular_columns/0.0.1", \n+            "tool_shed_repository": {\n+                "changeset_revision": "d43312f961cc", \n+                "name": "split_tabular_columns", \n+                "owner": "jjohnson", \n+                "tool_shed": "toolshed.g2.bx.psu.edu"\n+            }, \n+            "tool_state": "{\\"split_on\\": \\"\\\\\\" \\\\\\"\\", \\"input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"columns\\": \\"[\\\\\\"6\\\\\\"]\\", \\"__page__\\": 0}", \n+            "tool_version": "0.0.1", \n+            "type": "tool", \n+            "uuid": "d1e9833a-dfd7-4ef3-8db6-6ec99453bac7", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "13e7e5dd-05b9-4df7-bc0e-43c7f1e60d26"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "32e221b0-193d-4a31-87b4-940b6e1771fe"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r eb71034189fb repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Mar 02 15:42:24 2017 -0500
b
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<repositories description="This workflow requires a number of different repositories.">
+    <repository changeset_revision="34758ab8aaa4" name="unipept" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="d43312f961cc" name="split_tabular_columns" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="e84d1c3bf4fe" name="query_tabular" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="123b9ca5e26a" name="sqlite_to_tabular" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>