view Galaxy-Workflow-DNAse-footprints-singlesample-bamInput_wellington_hint_piq.ga @ 8:777faad85c7c draft default tip

Uploaded

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "DNAse-footprints-singlesample-bamInput_wellington_hint_piq", 
    "steps": {
        "0": {
            "annotation": "0", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "0", 
                    "name": "sorted Bam"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 226.383544921875, 
                "top": 220.94318389892578
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"sorted Bam\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "1": {
            "annotation": "2", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [], 
            "label": null, 
            "name": "Convert from BAM to BED", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bed"
                }
            ], 
            "position": {
                "left": 466.2727355957031, 
                "top": 210.88920211791992
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "bedtools_bamtobed", 
            "tool_state": "{\"__page__\": 0, \"option\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"input_source\": \"{\\\"input_type\\\": \\\"file\\\", \\\"__current_case__\\\": 1, \\\"input_file\\\": null}\", \"tag\": \"\\\"\\\"\", \"split\": \"\\\"False\\\"\", \"ed_score\": \"\\\"False\\\"\"}", 
            "tool_version": "BEDTOOLS: 2.17.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "2": {
            "annotation": "3", 
            "id": 2, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "piq", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "csv"
                }
            ], 
            "position": {
                "left": 1022.210205078125, 
                "top": 532.2102203369141
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "piq", 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "PIQ: 1.3", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "3": {
            "annotation": "4", 
            "id": 3, 
            "input_connections": {
                "fd_0|input": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "FSeq", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bed,wig"
                }
            ], 
            "position": {
                "left": 513.2613689899445, 
                "top": 375.875
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "fseq", 
            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"bed\\\"\", \"wiggleTrackStep\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"featLen\": \"\\\"600\\\"\", \"fd\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"threshold\": \"\\\"2.5\\\"\", \"fragSize\": \"\\\"0\\\"\"}", 
            "tool_version": "F-Seq: 1.85", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "4": {
            "annotation": "16", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Uniq", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1246.03125, 
                "top": 541.0170440673828
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "piq_uniq"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "uniq", 
            "tool_state": "{\"columnList\": \"\\\"1,2,3\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "7dcb1018-baa2-48a1-a0ee-478d8edced77"
        }, 
        "5": {
            "annotation": "6", 
            "id": 5, 
            "input_connections": {
                "input": {
                    "id": 3, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 389.2841033935547, 
                "top": 528.8863372802734
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "6": {
            "annotation": "8", 
            "id": 6, 
            "input_connections": {
                "input": {
                    "id": 5, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Compute", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 587.28125, 
                "top": 531.8834991455078
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Add_a_column1", 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2-c3\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "7": {
            "annotation": "9", 
            "id": 7, 
            "input_connections": {
                "input": {
                    "id": 6, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 788.2897644042969, 
                "top": 531.8834991455078
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4<-400\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "8": {
            "annotation": "10", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 784.7102355957031, 
                "top": 367.2670440673828
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "9": {
            "annotation": "11", 
            "id": 9, 
            "input_connections": {
                "input": {
                    "id": 8, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 779.8806762695312, 
                "top": 221.44318389892578
            }, 
            "post_job_actions": {
                "ChangeDatatypeActionout_file1": {
                    "action_arguments": {
                        "newtype": "bed"
                    }, 
                    "action_type": "ChangeDatatypeAction", 
                    "output_name": "out_file1"
                }, 
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c1=='chr1' or c1=='chr2'or c1=='chr3' or c1=='chr4' or c1=='chr5' or c1=='chr6' or c1=='chr7' or c1=='chr8' or c1=='chr9' or c1=='chr10' or c1=='chr11' or c1=='chr12' or c1=='chr13' or c1=='chr14' or c1=='chr15' or c1=='chr16' or c1=='chr17' or c1=='chr18' or c1=='chr19' or c1=='chr20' or c1=='chr21' or c1=='chr22' or c1=='chrX' or c1=='chrY'\\\"\", \"__page__\": 0}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "10": {
            "annotation": "12", 
            "id": 10, 
            "input_connections": {
                "bam_file": {
                    "id": 0, 
                    "output_name": "output"
                }, 
                "bed_file": {
                    "id": 9, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Wellington Footprints", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bed"
                }
            ], 
            "position": {
                "left": 984.9090881347656, 
                "top": 207.96306610107422
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "wellington_footprints", 
            "tool_state": "{\"__page__\": 0, \"bam_file\": \"null\", \"bed_file\": \"null\", \"__rerun_remap_job_id__\": null, \"fdrlimit\": \"\\\"0\\\"\"}", 
            "tool_version": "0.2.5", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "11": {
            "annotation": "13", 
            "id": 11, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output"
                }, 
                "region": {
                    "id": 9, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Hint", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bed"
                }
            ], 
            "position": {
                "left": 996.897705078125, 
                "top": 371.9545440673828
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "hint", 
            "tool_state": "{\"input\": \"null\", \"region\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "HINT: 1.1.1", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "12": {
            "annotation": "14", 
            "id": 12, 
            "input_connections": {
                "input": {
                    "id": 10, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Sort", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1225.9176025390625, 
                "top": 206.9545440673828
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "wellington_sorted"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "sort1", 
            "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "13": {
            "annotation": "15", 
            "id": 13, 
            "input_connections": {
                "input": {
                    "id": 11, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Sort", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1231.897705078125, 
                "top": 395.9460144042969
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "hint_sorted"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "sort1", 
            "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }
    }, 
    "uuid": "a1168692-fb6d-4143-b956-fe7f10370bec"
}