view Add_chr_to_first_column_of_a_6_columns_BED_file.ga @ 0:16fc7f46ee23 draft default tip

Uploaded

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Add 'chr' to first column of a BED file (must have 6 columns)", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "BED file"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 193
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"BED file\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Add column", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 423, 
                "top": 200
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "addValue", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Merge Columns", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 657, 
                "top": 211
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "mergeCols1", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "input": {
                    "id": 2, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 872, 
                "top": 205
            }, 
            "post_job_actions": {
                "ChangeDatatypeActionout_file1": {
                    "action_arguments": {
                        "newtype": "interval"
                    }, 
                    "action_type": "ChangeDatatypeAction", 
                    "output_name": "out_file1"
                }, 
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "added \"chr\" to chromosome name"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
            "tool_version": "1.0.2", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}