view Galaxy-Workflow-MiModD_example_workflow_1.ga @ 1:87bfe31ce878 default tip

workflows for MiModD 0.1.6
author Wolfgang Maier
date Thu, 04 Jun 2015 18:19:52 +0200
parents 9f64313f2ccb
children
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{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "MiModD example workflow 1", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Input Dataset"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 172, 
                "top": 176
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Input Dataset\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {
                "ref_genome": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "SNAP Read Alignment", 
            "outputs": [
                {
                    "name": "outputfile", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 359, 
                "top": 368
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "read_alignment", 
            "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "list_input_0|inputfile": {
                    "id": 1, 
                    "output_name": "outputfile"
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                "ref_genome": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Variant Calling", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "bcf"
                }
            ], 
            "position": {
                "left": 708, 
                "top": 364
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "variant_calling", 
            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "ifile": {
                    "id": 2, 
                    "output_name": "output_vcf"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Extract Variant Sites", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 1104.5, 
                "top": 227
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "extract_variants", 
            "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
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        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "ifile": {
                    "id": 2, 
                    "output_name": "output_vcf"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Coverage Statistics", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 1133, 
                "top": 455
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "coverage_stats", 
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            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "covfile": {
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                    "output_name": "output_vcf"
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                "list_input_0|bamfile": {
                    "id": 1, 
                    "output_name": "outputfile"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Deletion Prediction for paired-end data", 
            "outputs": [
                {
                    "name": "outputfile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 1031, 
                "top": 666
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "deletion_prediction", 
            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": [], 
            "uuid": "None"
        }
    }, 
    "uuid": "cd57b671-cca3-4667-8b2a-1e32d0e86d2c"
}