view Galaxy-Workflow-SADI-Docker_use_case.ga @ 1:47db0b303a50 default tip

Added annotations to workflow
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Mon, 07 Sep 2015 19:18:27 +0200
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{
    "a_galaxy_workflow": "true", 
    "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", 
    "format-version": "0.1", 
    "name": "SADI-Docker use case", 
    "steps": {
        "0": {
            "annotation": "Convert white spaces to tabs, so that Galaxy recognises the list of UniProt IDs as a column", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [], 
            "label": null, 
            "name": "Convert", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
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            "tool_id": "Convert characters1", 
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            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "658762bb-9052-4dd2-bb6b-e77613a6dcfe"
        }, 
        "1": {
            "annotation": "Convert UniProt identifiers to URIs: Add a column with the first part of the URI", 
            "id": 1, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Add column", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
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            "tool_id": "addValue", 
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            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "c2421757-1d5d-435c-ac9e-fb036ccd4448"
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        "2": {
            "annotation": "Convert UniProt identifiers to URIs", 
            "id": 2, 
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                "input1": {
                    "id": 1, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Merge Columns", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
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            "post_job_actions": {}, 
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            "tool_version": "1.0.1", 
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            "user_outputs": [], 
            "uuid": "63b4d2ff-0e1d-449d-aad5-a2ccd033d36a"
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        "3": {
            "annotation": "Obtain the UniProt URIs", 
            "id": 3, 
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                    "id": 2, 
                    "output_name": "out_file1"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
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            "post_job_actions": {}, 
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            "tool_id": "Cut1", 
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            "tool_version": "1.0.2", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "f3912f69-b561-4dd5-91f0-1e492e19bb9c"
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        "4": {
            "annotation": "Add a column with the URI of the SADI service input OWL class", 
            "id": 4, 
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                "input": {
                    "id": 3, 
                    "output_name": "out_file1"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Add column", 
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                    "name": "out_file1", 
                    "type": "input"
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            "uuid": "c01e5509-2a60-4ad4-848c-b31f9ccfc841"
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        "5": {
            "annotation": "Add a column with the URI of the SADI service input OWL class", 
            "id": 5, 
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                    "id": 3, 
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Add column", 
            "outputs": [
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                    "name": "out_file1", 
                    "type": "input"
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            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://openlifedata.org/uniprot_vocabulary:Resource\\\"\", \"iterate\": \"\\\"no\\\"\"}", 
            "tool_version": "1.0.0", 
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            "uuid": "98b1f088-3de5-4dbd-a655-63a630517e1a"
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        "6": {
            "annotation": "Convert to RDF, adding the triple rdf:type input OWL class", 
            "id": 6, 
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                    "output_name": "out_file1"
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            }, 
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            "name": "SADI - Tab-to-RDF", 
            "outputs": [
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                    "name": "output_file", 
                    "type": "rdf"
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        "7": {
            "annotation": "Convert to RDF, adding the triple rdf:type input OWL class", 
            "id": 7, 
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            "inputs": [], 
            "label": null, 
            "name": "SADI - Tab-to-RDF", 
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                    "name": "output_file", 
                    "type": "rdf"
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            "uuid": "217c654d-5353-4d93-a6de-c5c5bb205e64"
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            "id": 8, 
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                    "output_name": "output_file"
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            "inputs": [], 
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            "name": "SADI - RDF Format (Rapper)", 
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                    "name": "output_file", 
                    "type": "rdf"
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        "11": {
            "annotation": "Execute SADI service to obtain HGNC entries", 
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            "annotation": "Merge all the inputs and outputs in single RDF graph: SADI only decorates inputs with new triples, so we can keep track of the whole process via URIs", 
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}