changeset 0:eb71034189fb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
author galaxyp
date Thu, 02 Mar 2017 15:42:24 -0500
parents
children 338a6d724774
files 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
diffstat 5 files changed, 1403 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /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
@@ -0,0 +1,437 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "ABRF 2017:Taxonomy Comparison Workflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "PSM Report (Bering Strait)"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 296, 
+                "top": 186
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"PSM Report (Bering Strait)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "c404eaed-7c90-4b48-82c4-9083bdb6db29", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "0bfee776-11e1-4553-a7ee-25fd0c628891"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "PSM Report (Chukchi Sea)"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 352, 
+                "top": 596.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"PSM Report (Chukchi Sea)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "c6e42b4c-4116-48eb-92a2-bebdbceaba1d", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "0d4f355a-1f05-49a9-a5a3-2f58fc25ca32"
+                }
+            ]
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 2, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 453, 
+                "top": 335
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "e84d1c3bf4fe", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "90d1308d-cd0a-4dc7-8da8-eb1a311e3825", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "cb6d774d-7930-4c42-b3dd-7e523acc58a2"
+                }
+            ]
+        }, 
+        "3": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 3, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 562, 
+                "top": 646.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "e84d1c3bf4fe", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\": \"\\\"false\\\"\", \"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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "f512a71f-f718-4eca-9879-95c876274d57", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "b2c1c6ac-672f-471f-8f81-1e9d7aaf1b18"
+                }
+            ]
+        }, 
+        "4": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "id": 4, 
+            "input_connections": {
+                "peptide_src|input_tsv": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Unipept", 
+                    "name": "peptide_src"
+                }
+            ], 
+            "label": null, 
+            "name": "Unipept", 
+            "outputs": [
+                {
+                    "name": "output_json", 
+                    "type": "d3_hierarchy"
+                }, 
+                {
+                    "name": "output_tsv", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_csv", 
+                    "type": "csv"
+                }, 
+                {
+                    "name": "output_unmatched", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 754.5, 
+                "top": 327.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_csv": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_csv"
+                }, 
+                "HideDatasetActionoutput_unmatched": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_unmatched"
+                }, 
+                "RenameDatasetActionoutput_json": {
+                    "action_arguments": {
+                        "newname": "Unipept: TAXONOMY Phylogenetic Tree (Bering Strait)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_json"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "34758ab8aaa4", 
+                "name": "unipept", 
+                "owner": "galaxyp", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"outputs\": \"[\\\"tsv\\\", \\\"json\\\"]\", \"__rerun_remap_job_id__\": null, \"peptide_src\": \"{\\\"column\\\": \\\"1\\\", \\\"fmt\\\": \\\"tabular\\\", \\\"input_tsv\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"strict\": \"\\\"false\\\"\", \"unipept\": \"{\\\"allfields\\\": \\\"false\\\", \\\"extra\\\": \\\"false\\\", \\\"api\\\": \\\"pept2lca\\\", \\\"names\\\": \\\"true\\\", \\\"__current_case__\\\": 0, \\\"equate_il\\\": \\\"true\\\"}\"}", 
+            "tool_version": "2.0.1", 
+            "type": "tool", 
+            "uuid": "829dee5e-7a29-4dce-857a-2c73f5967fc6", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output_tsv", 
+                    "uuid": "3b30dfdc-5778-4862-8d14-819c4a1c81a5"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "output_json", 
+                    "uuid": "d1d13d17-c7b2-4ebc-a4e6-822b05a99eea"
+                }
+            ]
+        }, 
+        "5": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "id": 5, 
+            "input_connections": {
+                "peptide_src|input_tsv": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Unipept", 
+                    "name": "peptide_src"
+                }
+            ], 
+            "label": null, 
+            "name": "Unipept", 
+            "outputs": [
+                {
+                    "name": "output_json", 
+                    "type": "d3_hierarchy"
+                }, 
+                {
+                    "name": "output_tsv", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_csv", 
+                    "type": "csv"
+                }, 
+                {
+                    "name": "output_unmatched", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 869, 
+                "top": 628.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_csv": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_csv"
+                }, 
+                "HideDatasetActionoutput_unmatched": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_unmatched"
+                }, 
+                "RenameDatasetActionoutput_json": {
+                    "action_arguments": {
+                        "newname": "Unipept: TAXONOMY Phylogenetic Tree (Chukchi Sea)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_json"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "34758ab8aaa4", 
+                "name": "unipept", 
+                "owner": "galaxyp", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"outputs\": \"[\\\"tsv\\\", \\\"json\\\"]\", \"__rerun_remap_job_id__\": null, \"peptide_src\": \"{\\\"column\\\": \\\"1\\\", \\\"fmt\\\": \\\"tabular\\\", \\\"input_tsv\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"strict\": \"\\\"false\\\"\", \"unipept\": \"{\\\"allfields\\\": \\\"false\\\", \\\"extra\\\": \\\"false\\\", \\\"api\\\": \\\"pept2lca\\\", \\\"names\\\": \\\"true\\\", \\\"__current_case__\\\": 0, \\\"equate_il\\\": \\\"true\\\"}\"}", 
+            "tool_version": "2.0.1", 
+            "type": "tool", 
+            "uuid": "a9912f29-258c-4327-9b45-67cccb557cf3", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output_tsv", 
+                    "uuid": "cc2030a9-5328-445a-bc90-5ce555b57275"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "output_json", 
+                    "uuid": "d1495e86-d619-4bf5-b573-b0afcb5aebbc"
+                }
+            ]
+        }, 
+        "6": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 6, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "tables_1|table": {
+                    "id": 4, 
+                    "output_name": "output_tsv"
+                }, 
+                "tables_2|table": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "tables_3|table": {
+                    "id": 5, 
+                    "output_name": "output_tsv"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1342, 
+                "top": 298.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }, 
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Unipept: TAXONOMY GENUS PSMs Peptides (Bering Strait and Chukchi Sea)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "e84d1c3bf4fe", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_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\\\"}}, {\\\"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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "c8b14d06-f3a3-46db-b3c6-01f5c50bc16e", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "ea8853c6-d1e2-4c04-a795-4b1af5e50ff4"
+                }
+            ]
+        }
+    }, 
+    "uuid": "8fac309b-4ea6-4c20-9e40-651b2346b3e8"
+}
\ No newline at end of file
--- /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
@@ -0,0 +1,422 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "ABRF 2017 Workflow for Functional Comparison", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Gene Ontology Terms"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 177, 
+                "top": 188.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Gene Ontology Terms\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "6f5a7554-d201-4f17-8e47-8e07ead87e52", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "1e545169-c1d0-4da0-9f5d-09632dffbd6a"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Bering Strait Pept2Prot (extra fields) Normalized"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 181, 
+                "top": 264.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Bering Strait Pept2Prot (extra fields) Normalized\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "caae62e0-46f1-4f84-934f-31be41856bb0", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "27ccf52d-44c0-43eb-bf66-bee437cfbcfa"
+                }
+            ]
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Chukchi Sea Pept2Prot (extra fields) Normalized"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 185, 
+                "top": 354.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Chukchi Sea Pept2Prot (extra fields) Normalized\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "3c954f78-1ef3-4cae-bb4e-c768d9904506", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "67cf7d09-93cf-4e90-9f2c-1f9c61973cff"
+                }
+            ]
+        }, 
+        "3": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Bering Strait PSM Report"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 187, 
+                "top": 442.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Bering Strait PSM Report\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "c9826c72-36c9-498e-af09-3ba77ce79885", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "4c8327ee-cabc-46f6-a3fb-ecf84dca3b8f"
+                }
+            ]
+        }, 
+        "4": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Chukchi Sea PSM Report"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 190, 
+                "top": 523.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Chukchi Sea PSM Report\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "6f38f059-5513-4705-b3f0-ff2a3aef638e", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "2c42d9b6-7107-4354-81dd-40728115bbb1"
+                }
+            ]
+        }, 
+        "5": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 5, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "tables_1|table": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "tables_2|table": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "tables_3|table": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "tables_4|table": {
+                    "id": 4, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 440, 
+                "top": 230
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "BIOLOGICAL PROCESS COMPARISON"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "ae27dab228b8", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"go\\\", \\\"col_names\\\": \\\"aspect,go_id,description\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_id\\\"}, {\\\"__index__\\\": 1, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"aspect,go_id,description\\\"}]}, \\\"__index__\\\": 0, \\\"input_opts\\\": {\\\"linefilters\\\": []}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"chukchi\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 2, \\\"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\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 3, \\\"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_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 4, \\\"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\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\",\\\\ncount(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\n FROM go as g LEFT OUTER 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 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 = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "42fb8bde-03c9-4e9d-b003-55d01bb306d6", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "369c85d5-6d8f-45ca-8f55-01dddce5a4e9"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "sqlitedb", 
+                    "uuid": "fb8dd73d-95c9-48c8-945c-07adf0b13dab"
+                }
+            ]
+        }, 
+        "6": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "id": 6, 
+            "input_connections": {
+                "sqlitedb": {
+                    "id": 5, 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SQLite to tabular", 
+                    "name": "sqlitedb"
+                }
+            ], 
+            "label": null, 
+            "name": "SQLite to tabular", 
+            "outputs": [
+                {
+                    "name": "query_results", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 874, 
+                "top": 204
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionquery_results": {
+                    "action_arguments": {
+                        "newname": "MOLECULAR FUNCTION COMPARISON"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "query_results"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "78e9570fbe08", 
+                "name": "sqlite_to_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER 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 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 = 'molecular_function'\\\\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\\\"\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "uuid": "ee7d5bd3-d2c4-4653-bd55-fa236abfc7f8", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "query_results", 
+                    "uuid": "90cf3457-65be-474d-a43f-ead52ad50e21"
+                }
+            ]
+        }, 
+        "7": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "id": 7, 
+            "input_connections": {
+                "sqlitedb": {
+                    "id": 5, 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SQLite to tabular", 
+                    "name": "sqlitedb"
+                }
+            ], 
+            "label": null, 
+            "name": "SQLite to tabular", 
+            "outputs": [
+                {
+                    "name": "query_results", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 876, 
+                "top": 342
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionquery_results": {
+                    "action_arguments": {
+                        "newname": "CELLULAR COMPONENT COMPARISON"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "query_results"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "78e9570fbe08", 
+                "name": "sqlite_to_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER 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 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\\\"\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "uuid": "d0f27344-2721-47e3-891a-0a9288293945", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "query_results", 
+                    "uuid": "80f8307d-68d7-4a49-bae8-b43957dd3098"
+                }
+            ]
+        }, 
+        "8": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "id": 8, 
+            "input_connections": {
+                "sqlitedb": {
+                    "id": 5, 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SQLite to tabular", 
+                    "name": "sqlitedb"
+                }
+            ], 
+            "label": null, 
+            "name": "SQLite to tabular", 
+            "outputs": [
+                {
+                    "name": "query_results", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 883, 
+                "top": 457.5
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionquery_results": {
+                    "action_arguments": {
+                        "newname": "PEPTIDE PSM COUNTS COMPARISON"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "query_results"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "78e9570fbe08", 
+                "name": "sqlite_to_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "uuid": "a3b80420-6655-4acf-b62b-dcb4ac5d9c6e", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "query_results", 
+                    "uuid": "a9b9c19b-8ab2-4f08-9c1f-73e6991f58f9"
+                }
+            ]
+        }
+    }, 
+    "uuid": "9f54fdad-4b9b-4389-8c3a-4512f0cf8df5"
+}
\ No newline at end of file
--- /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
@@ -0,0 +1,311 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "ABRF UNIPEPT:Taxonomy Workflow Bering Strait", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "PSM Report"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 189, 
+                "top": 163
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"PSM Report\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "22470252-89e0-47c6-ba28-5efab1803316", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "8c57d953-0eca-4d62-8e5c-2ad994f7db4b"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 1, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 397, 
+                "top": 295
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "ae27dab228b8", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "b210efa3-4926-4e07-99e6-2619258d28a7", 
+            "workflow_outputs": [
+                {
+                    "label": "", 
+                    "output_name": "output", 
+                    "uuid": "15f7b9a0-5c26-4bbd-aa6b-e92746886a25"
+                }
+            ]
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "id": 2, 
+            "input_connections": {
+                "sqlitedb": {
+                    "id": 1, 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SQLite to tabular", 
+                    "name": "sqlitedb"
+                }
+            ], 
+            "label": null, 
+            "name": "SQLite to tabular", 
+            "outputs": [
+                {
+                    "name": "query_results", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 760.5, 
+                "top": 265.5
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionquery_results": {
+                    "action_arguments": {
+                        "newname": "Bering Strait PEPTIDEs with PSMs"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "query_results"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "78e9570fbe08", 
+                "name": "sqlite_to_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"sqlquery\": \"\\\"SELECT sequence as \\\\\\\"peptide\\\\\\\", count(id) as \\\\\\\"PSMs\\\\\\\"\\\\nFROM psm \\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95 \\\\nGROUP BY sequence\\\\nORDER BY sequence\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "uuid": "070a98b8-b69e-442d-94da-f0f99cf397f9", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "query_results", 
+                    "uuid": "11c53e11-5c81-41a3-af8b-9b90ccb6b45c"
+                }
+            ]
+        }, 
+        "3": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "id": 3, 
+            "input_connections": {
+                "peptide_src|input_tsv": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Unipept", 
+                    "name": "peptide_src"
+                }
+            ], 
+            "label": null, 
+            "name": "Unipept", 
+            "outputs": [
+                {
+                    "name": "output_json", 
+                    "type": "d3_hierarchy"
+                }, 
+                {
+                    "name": "output_tsv", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_csv", 
+                    "type": "csv"
+                }, 
+                {
+                    "name": "output_unmatched", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 732.5, 
+                "top": 367.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_csv": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_csv"
+                }, 
+                "HideDatasetActionoutput_unmatched": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_unmatched"
+                }, 
+                "RenameDatasetActionoutput_json": {
+                    "action_arguments": {
+                        "newname": "Unipept: TAXONOMY Phylogenetic Tree (Bering Strait)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_json"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "34758ab8aaa4", 
+                "name": "unipept", 
+                "owner": "galaxyp", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"outputs\": \"[\\\"tsv\\\", \\\"json\\\"]\", \"__rerun_remap_job_id__\": null, \"peptide_src\": \"{\\\"column\\\": \\\"1\\\", \\\"fmt\\\": \\\"tabular\\\", \\\"input_tsv\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"strict\": \"\\\"false\\\"\", \"unipept\": \"{\\\"allfields\\\": \\\"false\\\", \\\"extra\\\": \\\"false\\\", \\\"api\\\": \\\"pept2lca\\\", \\\"names\\\": \\\"true\\\", \\\"__current_case__\\\": 0, \\\"equate_il\\\": \\\"true\\\"}\"}", 
+            "tool_version": "2.0.1", 
+            "type": "tool", 
+            "uuid": "6163af00-e4d8-4aa8-8dd8-27d0f99489db", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output_tsv", 
+                    "uuid": "11b0f0a3-066b-4680-8628-927277c3bb57"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "output_json", 
+                    "uuid": "885b932a-4e21-40cf-a687-3075adcbbd9f"
+                }
+            ]
+        }, 
+        "4": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 4, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "tables_1|table": {
+                    "id": 3, 
+                    "output_name": "output_tsv"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1044, 
+                "top": 162
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }, 
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Unipept: TAXONOMY GENUS PSMs Peptides (Bering Strait)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "ae27dab228b8", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "4ac60e8a-cc65-48c8-9ea5-a26b35b90558", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "c618c51e-2f1e-437c-a570-981d2d07ea02"
+                }
+            ]
+        }
+    }, 
+    "uuid": "87aed6af-eb3b-4d42-99c0-e1a62fd59413"
+}
\ No newline at end of file
--- /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
@@ -0,0 +1,226 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "ABRF UNIPEPT: Peptide GO Annotation Step1", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "PSM Report"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 204, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"PSM Report\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "19976c04-5769-48c8-a26f-931d821db5df", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "62d54f79-3123-4816-98c8-2746e1570ec3"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "id": 1, 
+            "input_connections": {
+                "tables_0|table": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query Tabular", 
+                    "name": "add_to_database"
+                }
+            ], 
+            "label": null, 
+            "name": "Query Tabular", 
+            "outputs": [
+                {
+                    "name": "sqlitedb", 
+                    "type": "sqlite"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 432, 
+                "top": 203
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionsqlitedb": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sqlitedb"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "ae27dab228b8", 
+                "name": "query_tabular", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "uuid": "a8789ea6-f25f-4f27-b687-351356e81967", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "e27b945e-e194-469e-a99c-c9db87476262"
+                }
+            ]
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "id": 2, 
+            "input_connections": {
+                "peptide_src|input_tsv": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Unipept", 
+                    "name": "peptide_src"
+                }
+            ], 
+            "label": null, 
+            "name": "Unipept", 
+            "outputs": [
+                {
+                    "name": "output_json", 
+                    "type": "d3_hierarchy"
+                }, 
+                {
+                    "name": "output_tsv", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_csv", 
+                    "type": "csv"
+                }, 
+                {
+                    "name": "output_unmatched", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 738.5, 
+                "top": 200.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_csv": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_csv"
+                }, 
+                "HideDatasetActionoutput_json": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_json"
+                }, 
+                "HideDatasetActionoutput_unmatched": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_unmatched"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "34758ab8aaa4", 
+                "name": "unipept", 
+                "owner": "galaxyp", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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\\\"}\"}", 
+            "tool_version": "2.0.1", 
+            "type": "tool", 
+            "uuid": "cf10a931-a775-441b-a8d7-6e03e45fa9db", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output_tsv", 
+                    "uuid": "243231a1-d987-4331-ad40-d5f6c92bc828"
+                }
+            ]
+        }, 
+        "3": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/split_tabular_columns/split_tabular_columns/0.0.1", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 2, 
+                    "output_name": "output_tsv"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Split Tabular Columns", 
+                    "name": "input"
+                }
+            ], 
+            "label": null, 
+            "name": "Split Tabular Columns", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1051, 
+                "top": 200.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/split_tabular_columns/split_tabular_columns/0.0.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "d43312f961cc", 
+                "name": "split_tabular_columns", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"split_on\": \"\\\" \\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"columns\": \"[\\\"6\\\"]\", \"__page__\": 0}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "uuid": "d1e9833a-dfd7-4ef3-8db6-6ec99453bac7", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "13e7e5dd-05b9-4df7-bc0e-43c7f1e60d26"
+                }
+            ]
+        }
+    }, 
+    "uuid": "32e221b0-193d-4a31-87b4-940b6e1771fe"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Mar 02 15:42:24 2017 -0500
@@ -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>