Mercurial > repos > fcaramia > methylation_analysis_bismark

view Galaxy-Workflow-Differential_Methylation_Bismark.ga @ 15:d2ba233899b0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fcaramia
date Mon, 17 Jun 2013 21:50:56 -0400
parents 4eeda563e6c1
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "Compare Methylation levels of 2 samples", 
    "format-version": "0.1", 
    "name": "Differential_Methylation_Bismark", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [], 
            "name": "Bismark", 
            "outputs": [
                {
                    "name": "summary", 
                    "type": "txt"
                }, 
                {
                    "name": "output", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 198, 
                "top": 200
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6", 
            "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}", 
            "tool_version": "0.7.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [], 
            "name": "Bismark", 
            "outputs": [
                {
                    "name": "summary", 
                    "type": "txt"
                }, 
                {
                    "name": "output", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 200, 
                "top": 375
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6", 
            "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}", 
            "tool_version": "0.7.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "bamfile": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Methylation Extractor", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bedgraph"
                }, 
                {
                    "name": "summary", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 432.5, 
                "top": 218
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6", 
            "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}", 
            "tool_version": "0.7.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "bamfile": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Methylation Extractor", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bedgraph"
                }, 
                {
                    "name": "summary", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 432.5, 
                "top": 394
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6", 
            "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}", 
            "tool_version": "0.7.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "bedgraph": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Methylation by Region Converter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }, 
                {
                    "name": "summary", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 673, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1", 
            "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}", 
            "tool_version": "0.1.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "bedgraph": {
                    "id": 3, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Methylation by Region Converter", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }, 
                {
                    "name": "summary", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 674, 
                "top": 397
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1", 
            "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}", 
            "tool_version": "0.1.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "seg1": {
                    "id": 4, 
                    "output_name": "output"
                }, 
                "seg2": {
                    "id": 5, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Differential Methylation", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 993, 
                "top": 308
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/differential_methylation_tool/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"seg1\": \"null\", \"annot\": \"\\\"both\\\"\", \"seg2\": \"null\", \"fdr\": \"\\\"none\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}