view ngsap-vc/Haplotypecaller.ga @ 3:0d10255b5434 draft default tip

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author scisjnu123
date Thu, 03 Oct 2019 10:42:15 -0400
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{
    "a_galaxy_workflow": "true", 
    "annotation": "Haplotypecaller workflow.", 
    "format-version": "0.1", 
    "name": "Haplotypecaller", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Input Dataset"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
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                "top": 208.1666717529297
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            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Input Dataset\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": [], 
            "uuid": "b9fb671f-f07f-498c-8c85-619987501313"
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        "1": {
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            "id": 1, 
            "input_connections": {
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                    "id": 0, 
                    "output_name": "output"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "GATK", 
            "outputs": [
                {
                    "name": "rtc_output_intervals", 
                    "type": "gatk_interval"
                }, 
                {
                    "name": "ir_output_bam", 
                    "type": "bam"
                }, 
                {
                    "name": "br_table", 
                    "type": "tabular"
                }, 
                {
                    "name": "ac_plotsReportFile", 
                    "type": "pdf"
                }, 
                {
                    "name": "pr_output_bam", 
                    "type": "bam"
                }, 
                {
                    "name": "hc_output_gvcf", 
                    "type": "vcf"
                }, 
                {
                    "name": "gg_output_gvcf", 
                    "type": "vcf"
                }, 
                {
                    "name": "cg_output_vcf", 
                    "type": "vcf"
                }, 
                {
                    "name": "cv_output_vcf", 
                    "type": "vcf"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
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            ], 
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            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/gatk/gatk/3.4-0.d9", 
            "tool_state": "{\"__page__\": 0, \"cond_threads\": \"{\\\"cond_threads_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"ref_file\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"cond_BQSR\": \"{\\\"cond_BQSR_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"HaplotypeCaller\\\", \\\"cond_usage\\\": {\\\"emitRefConfidence\\\": \\\"GVCF\\\", \\\"__current_case__\\\": 0, \\\"cond_usage_selector\\\": \\\"GVCF\\\"}, \\\"optional_parameters\\\": {\\\"optional_parameters_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"cond_bam_input\\\": {\\\"input\\\": null, \\\"all_in_one\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 5}\", \"cond_intervals\": \"{\\\"cond_intervals_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", 
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    "uuid": "e4f99de3-d6b0-4554-9562-60b2b0eed2d3"
}