Mercurial > repos > iracooke > proteogenomics_msms_to_gff_workflow

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author iracooke
date Wed, 19 Mar 2014 00:14:32 -0400
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{
    "a_galaxy_workflow": "true", 
    "annotation": "Creates a protein database from a 6-frame translation of a genome, and from predicted transcripts, then searches msms data using this database and maps peptides back to the genome", 
    "format-version": "0.1", 
    "name": "Proteogenomics Map Peptides to GFF", 
    "steps": {
        "0": {
            "annotation": "MSMSData", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "MSMSData", 
                    "name": "MSMS Data"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 200
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"MSMS Data\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Genome"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 206, 
                "top": 371
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Genome\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Predicted Genes"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 207, 
                "top": 616
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Predicted Genes\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "type|input": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "msconvert3", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "mzml"
                }
            ], 
            "position": {
                "left": 967, 
                "top": 314
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iracooke/msconvert/msconvert3/0.2.1", 
            "tool_state": "{\"__page__\": 0, \"filtering\": \"{\\\"filtering_use\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"settings\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/vagrant/galaxy-dist/database/files/000/dataset_27.dat\\\"\", \"__rerun_remap_job_id__\": null, \"output_type\": \"\\\"mzML\\\"\", \"type\": \"{\\\"input_type\\\": \\\"mgf\\\", \\\"__current_case__\\\": 2, \\\"input\\\": null}\"}", 
            "tool_version": "0.2.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "fasta_file": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Generate 6-frame translation", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 554, 
                "top": 570
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iracooke/sixframe_translate/sixframe_translate/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"strip_header\": \"\\\"True\\\"\", \"fasta_file\": \"null\", \"coords\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/vagrant/galaxy-dist/database/files/000/dataset_27.dat\\\"\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "gff_file": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Extract proteins from gff3", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 524, 
                "top": 876
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iracooke/proteindb_from_gff3/proteindb_from_gff3/1.0.1", 
            "tool_state": "{\"gff_file\": \"null\", \"coords\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/vagrant/galaxy-dist/database/files/000/dataset_27.dat\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
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        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "input1": {
                    "id": 5, 
                    "output_name": "output"
                }, 
                "queries_0|input2": {
                    "id": 4, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Concatenate datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 898, 
                "top": 590
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "cat1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/vagrant/galaxy-dist/database/files/000/dataset_27.dat\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "fasta_file": {
                    "id": 6, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Generate protein decoy sequences", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1092, 
                "top": 448
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iracooke/make_protein_decoys/make_decoy/1.0.0", 
            "tool_state": "{\"prefix_string\": \"\\\"decoy_\\\"\", \"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/home/vagrant/galaxy-dist/database/files/000/dataset_27.dat\\\"\", \"__rerun_remap_job_id__\": null, \"append\": \"\\\"True\\\"\"}", 
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            "annotation": "", 
            "id": 8, 
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                    "output_name": "output"
                }, 
                "input_file": {
                    "id": 3, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "MSGF+ MSMS Search", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "mzid"
                }
            ], 
            "position": {
                "left": 1389, 
                "top": 313
            }, 
            "post_job_actions": {}, 
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                "input_file": {
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                    "output_name": "output"
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            }, 
            "inputs": [], 
            "name": "Peptide Prophet", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "peptideprophet_pepxml"
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                "top": 250
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            "outputs": [
                {
                    "name": "output", 
                    "type": "protxml"
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            "inputs": [], 
            "name": "ProtXML to GFF", 
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}