view BamExonCoverage1X10X20X30X.ga @ 1:ae6eb099d5b8 draft

Uploaded
author getiria-onsongo
date Thu, 06 Dec 2012 12:27:49 -0500
parents
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "BamExonCoverage1X10X20X30X", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "mapped reads: .BAM"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 197.4166259765625, 
                "top": 357.41667175292969
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"mapped reads: .BAM\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "targeted interval: .bed"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 1202, 
                "top": 778
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"targeted interval: .bed\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "reference_source|input_bams_0|input_bam": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "MPileup", 
            "outputs": [
                {
                    "name": "output_mpileup", 
                    "type": "pileup"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 454, 
                "top": 237
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "samtools_mpileup", 
            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", 
            "tool_version": "0.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "input": {
                    "id": 2, 
                    "output_name": "output_mpileup"
                }
            }, 
            "inputs": [], 
            "name": "Compute", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 727, 
                "top": 372
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Add_a_column1", 
            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2-1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"round\": \"\\\"yes\\\"\", \"input\": \"null\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 3, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 963, 
                "top": 322
            }, 
            "post_job_actions": {
                "ChangeDatatypeActionout_file1": {
                    "action_arguments": {
                        "newtype": "interval"
                    }, 
                    "action_type": "ChangeDatatypeAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"columnList\": \"\\\"c1,c7,c2,c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "input": {
                    "id": 4, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1184, 
                "top": 422
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 1\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input2": {
                    "id": 5, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Coverage", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "interval"
                }
            ], 
            "position": {
                "left": 1485, 
                "top": 422
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "gops_coverage_1", 
            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "input": {
                    "id": 5, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1439, 
                "top": 608
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 10\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input2": {
                    "id": 7, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Coverage", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "interval"
                }
            ], 
            "position": {
                "left": 1699, 
                "top": 614
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "gops_coverage_1", 
            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "", 
            "id": 9, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1718, 
                "top": 773
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 20\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "", 
            "id": 10, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input2": {
                    "id": 9, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Coverage", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "interval"
                }
            ], 
            "position": {
                "left": 1944, 
                "top": 773
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "gops_coverage_1", 
            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "11": {
            "annotation": "", 
            "id": 11, 
            "input_connections": {
                "input": {
                    "id": 9, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1922, 
                "top": 976
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 30\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "12": {
            "annotation": "", 
            "id": 12, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input2": {
                    "id": 11, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Coverage", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "interval"
                }
            ], 
            "position": {
                "left": 2158, 
                "top": 977
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "gops_coverage_1", 
            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "13": {
            "annotation": "", 
            "id": 13, 
            "input_connections": {
                "file_chooser_0|input": {
                    "id": 10, 
                    "output_name": "output"
                }, 
                "file_chooser_1|input": {
                    "id": 12, 
                    "output_name": "output"
                }, 
                "input1": {
                    "id": 6, 
                    "output_name": "output"
                }, 
                "input2": {
                    "id": 8, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Column Join", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 2387, 
                "top": 474
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "Coverage1X10X20X30X"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "column_join", 
            "tool_state": "{\"input2\": \"null\", \"hinge\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"input1\": \"null\", \"__page__\": 0, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"file_chooser\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\", \\\"2\\\", \\\"3\\\", \\\"5\\\"]}\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}