view Galaxy-Workflow-Virana.ga @ 50:335fcf29f08a draft

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{
    "a_galaxy_workflow": "true", 
    "annotation": "simple virana test workflow", 
    "format-version": "0.1", 
    "name": "Virana", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Input Dataset"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 200
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Input Dataset\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [], 
            "name": "Virana References", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 200, 
                "top": 283
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vref_fasta/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"refseq\": \"null\", \"zipped\": \"\\\"False\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
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        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "input": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Virana DNAIndex", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "bwa_index"
                }
            ], 
            "position": {
                "left": 434, 
                "top": 200
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vmap_dnaindex/1.0.0", 
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            "tool_version": "1.0.0", 
            "type": "tool", 
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        "3": {
            "annotation": "", 
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            "input_connections": {
                "index": {
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                    "output_name": "output"
                }, 
                "reads": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Virana DNAMap", 
            "outputs": [
                {
                    "name": "hit_output", 
                    "type": "hit_bz2"
                }, 
                {
                    "name": "bam_output", 
                    "type": "bam"
                }, 
                {
                    "name": "sam_output", 
                    "type": "sam"
                }, 
                {
                    "name": "qual_output", 
                    "type": "qual"
                }, 
                {
                    "name": "tax_output", 
                    "type": "tax"
                }
            ], 
            "position": {
                "left": 668, 
                "top": 200
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vmap_dnamap/1.0.0", 
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            "tool_version": "1.0.0", 
            "type": "tool", 
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        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "references": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "virana_hits": {
                    "id": 3, 
                    "output_name": "hit_output"
                }
            }, 
            "inputs": [], 
            "name": "Virana Homologous Groups", 
            "outputs": [
                {
                    "name": "hom_output", 
                    "type": "hom_reg"
                }, 
                {
                    "name": "stat_output", 
                    "type": "reg_stats"
                }
            ], 
            "position": {
                "left": 902, 
                "top": 200
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vhom_region/1.1.1", 
            "tool_state": "{\"max_gap_length\": \"\\\"25\\\"\", \"__page__\": 0, \"virana_hits\": \"null\", \"filter\": \"[]\", \"reference_database_filter\": \"null\", \"word_length\": \"\\\"7\\\"\", \"references\": \"null\", \"ambiguity_cutoff\": \"\\\"0.3\\\"\", \"min_read_number\": \"\\\"5\\\"\", \"min_region_length\": \"\\\"50\\\"\", \"cdna\": \"null\"}", 
            "tool_version": "1.1.1", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}