view Galaxy-Workflow-MiModD_example_workflow_3.ga @ 1:87bfe31ce878 default tip

workflows for MiModD 0.1.6

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "MiModD example workflow 3", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Reference Genome"
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            ], 
            "label": null, 
            "name": "Input dataset", 
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            "position": {
                "left": 200, 
                "top": 391
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Reference Genome\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": [], 
            "uuid": "None"
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        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Hawaiian strain variants file"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
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            "position": {
                "left": 707.5, 
                "top": 335
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Hawaiian strain variants file\"}", 
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        "2": {
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                    "output_name": "output"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "SNAP Read Alignment", 
            "outputs": [
                {
                    "name": "outputfile", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 334, 
                "top": 607
            }, 
            "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}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"single\\\", \\\"__current_case__\\\": 0}}]\", \"__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\"}", 
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                    "output_name": "outputfile"
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                    "id": 0, 
                    "output_name": "output"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Variant Calling", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "bcf"
                }
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            "position": {
                "left": 692, 
                "top": 607
            }, 
            "post_job_actions": {}, 
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            "annotation": "", 
            "id": 4, 
            "input_connections": {
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                "sitesinfo_0|pre_vcf": {
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                    "output_name": "output"
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            }, 
            "inputs": [], 
            "label": null, 
            "name": "Extract Variant Sites", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "vcf"
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            "position": {
                "left": 973.5, 
                "top": 483
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            "post_job_actions": {}, 
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            "id": 5, 
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                    "output_name": "output_vcf"
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            "inputs": [], 
            "label": null, 
            "name": "Coverage Statistics", 
            "outputs": [
                {
                    "name": "output_vcf", 
                    "type": "tabular"
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            ], 
            "position": {
                "left": 1054, 
                "top": 726
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            "post_job_actions": {}, 
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            "type": "tool", 
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            "id": 6, 
            "input_connections": {
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                    "output_name": "output_vcf"
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            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Prepare variant data for mapping", 
                    "name": "sample"
                }, 
                {
                    "description": "runtime parameter for tool Prepare variant data for mapping", 
                    "name": "run"
                }, 
                {
                    "description": "runtime parameter for tool Prepare variant data for mapping", 
                    "name": "run"
                }
            ], 
            "label": null, 
            "name": "Prepare variant data for mapping", 
            "outputs": [
                {
                    "name": "ofile", 
                    "type": "vcf"
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                {
                    "name": "dictfile", 
                    "type": "tabular"
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            "position": {
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                "top": 200
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            "post_job_actions": {}, 
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            "tool_version": "1.0.0", 
            "type": "tool", 
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            "uuid": "6225f501-6db8-4c83-ad42-59a8f1330a55"
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    "uuid": "0a619835-3d93-489f-8d0d-93a567536404"
}