Repository 'sadi_docker_workflow'
hg clone https://toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sadi_docker_workflow

Changeset 1:47db0b303a50 (2015-09-07)
Previous changeset 0:22be3a551998 (2015-09-04)
Commit message:
Added annotations to workflow
added:
Galaxy-Workflow-SADI-Docker_use_case.ga
b
diff -r 22be3a551998 -r 47db0b303a50 Galaxy-Workflow-SADI-Docker_use_case.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-SADI-Docker_use_case.ga Mon Sep 07 19:18:27 2015 +0200
[
b'@@ -0,0 +1,520 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "The workflow answers the following question: Given a set of UniProt proteins, which ones are related to PubMed abstracts containing the term ``brain\'\', and what are they KEGG entries? The workflow starts from a simple list of UniProt identifiers, and retrieves different datasets from a regular SADI service (to obtain KEGG entries) and a set of 3 OpenLifeData2SADI services (to obtain PubMed abstracts). The results are then merged and queried to obtain the KEGG entries of proteins that are related to PubMed abstracts that contain the term", \n+    "format-version": "0.1", \n+    "name": "SADI-Docker use case", \n+    "steps": {\n+        "0": {\n+            "annotation": "Convert white spaces to tabs, so that Galaxy recognises the list of UniProt IDs as a column", \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Convert", \n+            "outputs": [\n+                {\n+                    "name": "out_file1", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 204.9895977973938, \n+                "top": 202.90626764297485\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "Convert characters1", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"condense\\": \\"\\\\\\"True\\\\\\"\\", \\"strip\\": \\"\\\\\\"True\\\\\\"\\", \\"input\\": \\"null\\", \\"convert_from\\": \\"\\\\\\"s\\\\\\"\\"}", \n+            "tool_version": "1.0.0", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "658762bb-9052-4dd2-bb6b-e77613a6dcfe"\n+        }, \n+        "1": {\n+            "annotation": "Convert UniProt identifiers to URIs: Add a column with the first part of the URI", \n+            "id": 1, \n+            "input_connections": {\n+                "input": {\n+                    "id": 0, \n+                    "output_name": "out_file1"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Add column", \n+            "outputs": [\n+                {\n+                    "name": "out_file1", \n+                    "type": "input"\n+                }\n+            ], \n+            "position": {\n+                "left": 199.9895977973938, \n+                "top": 335.9097466468811\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "addValue", \n+            "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"exp\\": \\"\\\\\\"http://openlifedata.org/uniprot:\\\\\\"\\", \\"iterate\\": \\"\\\\\\"no\\\\\\"\\"}", \n+            "tool_version": "1.0.0", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "c2421757-1d5d-435c-ac9e-fb036ccd4448"\n+        }, \n+        "2": {\n+            "annotation": "Convert UniProt identifiers to URIs", \n+            "id": 2, \n+            "input_connections": {\n+                "input1": {\n+                    "id": 1, \n+                    "output_name": "out_file1"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Merge Columns", \n+            "outputs": [\n+                {\n+                    "name": "out_file1", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 201.96875429153442, \n+                "top": 473.91322565078735\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "mergeCols1", \n+            "tool_state": "{\\"__page__\\": 0, \\"input1\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"col2\\": \\"\\\\\\"\\\\\\"\\", \\"col1\\": \\"\\\\\\"\\\\\\"\\", \\"columns\\": \\"[]\\"}", \n+            "tool_version": "1.0.1", \n+            "type"'..b'SADI only decorates inputs with new triples, so we can keep track of the whole process via URIs", \n+            "id": 14, \n+            "input_connections": {\n+                "input_files_0|input_file": {\n+                    "id": 13, \n+                    "output_name": "output"\n+                }, \n+                "input_files_1|input_file": {\n+                    "id": 12, \n+                    "output_name": "output"\n+                }, \n+                "input_files_2|input_file": {\n+                    "id": 11, \n+                    "output_name": "output"\n+                }, \n+                "input_files_3|input_file": {\n+                    "id": 10, \n+                    "output_name": "output"\n+                }, \n+                "input_files_4|input_file": {\n+                    "id": 9, \n+                    "output_name": "output_file"\n+                }, \n+                "input_files_5|input_file": {\n+                    "id": 8, \n+                    "output_name": "output_file"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "SADI - Merge RDF Graphs", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "rdf"\n+                }\n+            ], \n+            "position": {\n+                "left": 1125.9965252876282, \n+                "top": 318.91319513320923\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "SADI-Docker-mergeRDFgraphs", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input_files\\": \\"[{\\\\\\"__index__\\\\\\": 0, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 1, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 2, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 3, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 4, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 5, \\\\\\"input_file\\\\\\": null}]\\"}", \n+            "tool_version": "0.1", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "7c24dd55-3032-4329-9fa3-734c963d8ed2"\n+        }, \n+        "15": {\n+            "annotation": "Query the merged RDF graph with the actual question", \n+            "id": 15, \n+            "input_connections": {\n+                "ontology": {\n+                    "id": 14, \n+                    "output_name": "output_file"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "SADI - Execute an SPARQL query against an RDF file", \n+            "outputs": [\n+                {\n+                    "name": "output", \n+                    "type": "html"\n+                }\n+            ], \n+            "position": {\n+                "left": 1439.993106842041, \n+                "top": 461.92015266418457\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "SADI-Docker-SPARQLGalaxy", \n+            "tool_state": "{\\"out_format\\": \\"\\\\\\"html\\\\\\"\\", \\"__page__\\": 0, \\"pasted_query\\": \\"\\\\\\"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \\\\\\\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\\\\\\\nPREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#>\\\\\\\\nPREFIX lsrn: <http://purl.oclc.org/SADI/LSRN/>\\\\\\\\n\\\\\\\\nSELECT ?protein ?label ?KEGG\\\\\\\\nWHERE { \\\\\\\\n?protein rdf:type lsrn:UniProt_Record . \\\\\\\\n?protein sadi:isEncodedBy ?KEGG . \\\\\\\\n?protein ?prot2hgnc ?hgnc . \\\\\\\\n?hgnc ?hgnc2omim ?omim . \\\\\\\\n?omim ?omim2pubmed ?pubmed . \\\\\\\\n?pubmed rdfs:label ?label . \\\\\\\\nFILTER (regex (?label, \'brain\'))\\\\\\\\n}\\\\\\"\\", \\"ontology\\": \\"null\\", \\"__rerun_remap_job_id__\\": null}", \n+            "tool_version": "0.1", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "9a453f8c-370e-4ab7-8e45-73cbba721db9"\n+        }\n+    }, \n+    "uuid": "8796e5be-1c91-4f91-9946-02a09a79401d"\n+}\n\\ No newline at end of file\n'