{
    "a_galaxy_workflow": "true",
    "annotation": "This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.",
    "creator": [
        {
            "class": "Person",
            "identifier": "https://orcid.org/0000-0002-9464-6640",
            "name": "Wolfgang Maier"
        }
    ],
    "format-version": "0.1",
    "license": "MIT",
    "name": "COVID-19: variation analysis reporting",
    "release": "0.3.4",
    "steps": {
        "0": {
            "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling",
                    "name": "Variation data to report"
                }
            ],
            "label": "Variation data to report",
            "name": "Input dataset collection",
            "outputs": [],
            "position": {
                "left": 10.28125,
                "top": 34.08333333333334
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"tag\": null, \"collection_type\": \"list\"}",
            "tool_version": null,
            "type": "data_collection_input",
            "uuid": "577438f0-38b1-4fc1-9145-935566d62347",
            "when": null,
            "workflow_outputs": []
        },
        "1": {
            "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.",
                    "name": "AF Filter"
                }
            ],
            "label": "AF Filter",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 5.3125,
                "top": 186.91145833333331
            },
            "tool_id": null,
            "tool_state": "{\"default\": 0.05, \"parameter_type\": \"float\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "2e5a5b38-c204-45a2-98e2-e113bce5a14b",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "af_filter_threshold",
                    "output_name": "output",
                    "uuid": "e55d47c5-7ea0-45c4-8844-47bf29b88542"
                }
            ]
        },
        "2": {
            "annotation": "Depth Filter. This is the minimum depth of all alignments at a variant site. ",
            "content_id": null,
            "errors": null,
            "id": 2,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Depth Filter. This is the minimum depth of all alignments at a variant site. ",
                    "name": "DP Filter"
                }
            ],
            "label": "DP Filter",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 0.78125,
                "top": 284.9270833333333
            },
            "tool_id": null,
            "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "c7fc64c7-51c7-465b-9184-ca834d4cf6b2",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "dp_filter_threshold",
                    "output_name": "output",
                    "uuid": "220a9662-8b6f-4161-8539-ecb613b4892a"
                }
            ]
        },
        "3": {
            "annotation": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.",
            "content_id": null,
            "errors": null,
            "id": 3,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.",
                    "name": "DP_ALT Filter"
                }
            ],
            "label": "DP_ALT Filter",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 0.0,
                "top": 367.42708333333337
            },
            "tool_id": null,
            "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "145bbc55-8893-413d-9620-f3d85e65527a",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "dp_alt_filter_threshold",
                    "output_name": "output",
                    "uuid": "7f7b09f6-e4e5-43af-881b-f336906bcb91"
                }
            ]
        },
        "4": {
            "annotation": "A custom tabular file mapping NCBI RefSeq Protein identifiers as used by snpEff version 4.5covid19 to their commonly used names. Can be obtained from https://doi.org/10.5281/zenodo.4555734",
            "content_id": null,
            "errors": null,
            "id": 4,
            "input_connections": {},
            "inputs": [
                {
                    "description": "A custom tabular file mapping NCBI RefSeq Protein identifiers as used by snpEff version 4.5covid19 to their commonly used names. Can be obtained from https://doi.org/10.5281/zenodo.4555734",
                    "name": "gene products translations"
                }
            ],
            "label": "gene products translations",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 690.015625,
                "top": 38.41145833333334
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "8b89e674-9012-4f66-a59a-ce05d2fe4223",
            "when": null,
            "workflow_outputs": []
        },
        "5": {
            "annotation": "Number of Clusters to use in Variant Frequency Plot.",
            "content_id": null,
            "errors": null,
            "id": 5,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Number of Clusters to use in Variant Frequency Plot.",
                    "name": "Number of Clusters"
                }
            ],
            "label": "Number of Clusters",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 3413.578125,
                "top": 671.9114583333334
            },
            "tool_id": null,
            "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "5ca7b1a7-e1ee-4b52-aab4-eaf23949e1da",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "plot_number_of_clusters",
                    "output_name": "output",
                    "uuid": "c02cc297-3f36-4f78-bede-3aa378436672"
                }
            ]
        },
        "6": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
            "errors": null,
            "id": 6,
            "input_connections": {
                "input": {
                    "id": 0,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "SnpSift Filter",
            "outputs": [
                {
                    "name": "output",
                    "type": "vcf"
                }
            ],
            "position": {
                "left": 246.65625,
                "top": 32.08333333333334
            },
            "post_job_actions": {},
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "5fab4f81391d",
                "name": "snpsift",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": \"DP >= 1\"}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "4.3+t.galaxy1",
            "type": "tool",
            "uuid": "386eb313-89c1-47df-bd3d-976780eff740",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "prefiltered_variants",
                    "output_name": "output",
                    "uuid": "498b63d3-2449-4633-b9a4-360553d14844"
                }
            ]
        },
        "7": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
            "errors": null,
            "id": 7,
            "input_connections": {
                "components_1|param_type|component_value": {
                    "id": 1,
                    "output_name": "output"
                },
                "components_3|param_type|component_value": {
                    "id": 2,
                    "output_name": "output"
                },
                "components_5|param_type|component_value": {
                    "id": 3,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Compose text parameter value",
            "outputs": [
                {
                    "name": "out1",
                    "type": "expression.json"
                }
            ],
            "position": {
                "left": 245.0,
                "top": 156.36458333333331
            },
            "post_job_actions": {
                "HideDatasetActionout1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out1"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
            "tool_shed_repository": {
                "changeset_revision": "e188c9826e0f",
                "name": "compose_text_param",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"( ( DP4[2] + DP4[3] ) < ( \"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" * DP ) ) | ( DP < \"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" ) | ( ( AF * DP ) < ( \"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" - 0.5 ) )\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.1.1",
            "type": "tool",
            "uuid": "ec1a4872-b9bc-41f0-8675-1f26fdd19f16",
            "when": null,
            "workflow_outputs": []
        },
        "8": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
            "errors": null,
            "id": 8,
            "input_connections": {
                "components_1|param_type|component_value": {
                    "id": 1,
                    "output_name": "output"
                },
                "components_3|param_type|component_value": {
                    "id": 2,
                    "output_name": "output"
                },
                "components_5|param_type|component_value": {
                    "id": 3,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Compose text parameter value",
            "outputs": [
                {
                    "name": "out1",
                    "type": "expression.json"
                }
            ],
            "position": {
                "left": 241.71875,
                "top": 463.83333333333337
            },
            "post_job_actions": {
                "HideDatasetActionout1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out1"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
            "tool_shed_repository": {
                "changeset_revision": "e188c9826e0f",
                "name": "compose_text_param",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"min_af_\"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_\"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_alt_\"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.1.1",
            "type": "tool",
            "uuid": "c9916563-c914-4f5f-90c6-d6c7619e1a98",
            "when": null,
            "workflow_outputs": []
        },
        "9": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
            "errors": null,
            "id": 9,
            "input_connections": {
                "filter_expression|expr": {
                    "id": 7,
                    "output_name": "out1"
                },
                "filtering|add_filter": {
                    "id": 8,
                    "output_name": "out1"
                },
                "input": {
                    "id": 6,
                    "output_name": "output"
                }
            },
            "inputs": [
                {
                    "description": "runtime parameter for tool SnpSift Filter",
                    "name": "filter_expression"
                },
                {
                    "description": "runtime parameter for tool SnpSift Filter",
                    "name": "filtering"
                }
            ],
            "label": null,
            "name": "SnpSift Filter",
            "outputs": [
                {
                    "name": "output",
                    "type": "vcf"
                }
            ],
            "position": {
                "left": 477.421875,
                "top": 322.0677083333333
            },
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "Filtered variants"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "5fab4f81391d",
                "name": "snpsift",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"add_filter\", \"__current_case__\": 3, \"add_filter\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "4.3+t.galaxy1",
            "type": "tool",
            "uuid": "9a6cb40d-476b-4096-adcc-cb601398d0b4",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "filtered_variants",
                    "output_name": "output",
                    "uuid": "d6db8dad-1774-4ec8-a858-26b17a287252"
                }
            ]
        },
        "10": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
            "errors": null,
            "id": 10,
            "input_connections": {
                "input": {
                    "id": 9,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "SnpSift Extract Fields",
            "outputs": [
                {
                    "name": "output",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 713.4375,
                "top": 219.05208333333331
            },
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "Filtered extracted variants"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "5fab4f81391d",
                "name": "snpsift",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID DP4[2] DP4[3]\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": true, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "4.3+t.galaxy0",
            "type": "tool",
            "uuid": "085e8f20-3eea-4d97-8e52-6e8a9aa3fbd7",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "filtered_extracted_variants",
                    "output_name": "output",
                    "uuid": "578ee06f-e803-42e2-8afe-b9e88f465cdb"
                }
            ]
        },
        "11": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
            "errors": null,
            "id": 11,
            "input_connections": {
                "original_file": {
                    "id": 10,
                    "output_name": "output"
                },
                "replace_information": {
                    "id": 4,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Replace column",
            "outputs": [
                {
                    "name": "outfile_replace",
                    "type": "txt"
                }
            ],
            "position": {
                "left": 944.3125,
                "top": 83.03645833333331
            },
            "post_job_actions": {
                "ChangeDatatypeActionoutfile_replace": {
                    "action_arguments": {
                        "newtype": "tabular"
                    },
                    "action_type": "ChangeDatatypeAction",
                    "output_name": "outfile_replace"
                },
                "RenameDatasetActionoutfile_replace": {
                    "action_arguments": {
                        "newname": "Extracted variants with filtered and renamed effects"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile_replace"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
            "tool_shed_repository": {
                "changeset_revision": "d533e4b75800",
                "name": "replace_column_by_key_value_file",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column_replace\": \"16\", \"delimiter\": \"tab\", \"original_file\": {\"__class__\": \"ConnectedValue\"}, \"pass_comments\": \"#\", \"replace_information\": {\"__class__\": \"ConnectedValue\"}, \"skip_lines\": \"1\", \"unknowns_strategy\": \"skip\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.2",
            "type": "tool",
            "uuid": "0850f6d5-ff1f-47f9-8e49-b7eb5782828a",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "filtered_and_renamed_effects",
                    "output_name": "outfile_replace",
                    "uuid": "25460c36-c35c-4233-97ba-ec0a7aec39e4"
                }
            ]
        },
        "12": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
            "errors": null,
            "id": 12,
            "input_connections": {
                "input": {
                    "id": 11,
                    "output_name": "outfile_replace"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Compute",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "input"
                }
            ],
            "position": {
                "left": 1164.734375,
                "top": 240.34895833333331
            },
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Extracted variants with filtered and renamed effects and AF recalculated"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
            "tool_shed_repository": {
                "changeset_revision": "aff5135563c6",
                "name": "column_maker",
                "owner": "devteam",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"expressions\": [{\"__index__\": 0, \"cond\": \"c7\", \"add_column\": {\"mode\": \"I\", \"__current_case__\": 1, \"pos\": \"8\"}, \"new_column_name\": \"AFcaller\"}, {\"__index__\": 1, \"cond\": \"round((c18 + c19) / c6, 6)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"7\"}, \"new_column_name\": \"AF\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.1",
            "type": "tool",
            "uuid": "c457f29e-dea5-449a-84c4-4b192da88257",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "af_recalculated",
                    "output_name": "out_file1",
                    "uuid": "86d866eb-b5ff-409c-aaee-d23deac15a47"
                }
            ]
        },
        "13": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 13,
            "input_connections": {
                "in_file": {
                    "id": 12,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 1331.15625,
                "top": 20.583333333333343
            },
            "post_job_actions": {
                "RenameDatasetActionout_file": {
                    "action_arguments": {
                        "newname": "Collapsed effects (Datamash on all variants)"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"1,2,3,4,5,6,7,8,9,10\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"collapse\", \"op_column\": \"11\"}, {\"__index__\": 1, \"op_name\": \"collapse\", \"op_column\": \"12\"}, {\"__index__\": 2, \"op_name\": \"collapse\", \"op_column\": \"13\"}, {\"__index__\": 3, \"op_name\": \"collapse\", \"op_column\": \"14\"}, {\"__index__\": 4, \"op_name\": \"collapse\", \"op_column\": \"15\"}, {\"__index__\": 5, \"op_name\": \"collapse\", \"op_column\": \"16\"}, {\"__index__\": 6, \"op_name\": \"collapse\", \"op_column\": \"17\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "ec8aca39-fe1f-404a-9460-7a960cec37e6",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "collapsed_effects",
                    "output_name": "out_file",
                    "uuid": "995044cd-d883-451e-b8a0-6905967f636b"
                }
            ]
        },
        "14": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "errors": null,
            "id": 14,
            "input_connections": {
                "infile": {
                    "id": 13,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Replace",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 1681.234375,
                "top": 0.0
            },
            "post_job_actions": {
                "RenameDatasetActionoutfile": {
                    "action_arguments": {
                        "newname": "Extracted variants with highest impact effects"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\s]+\", \"replace_pattern\": \"\\\\t$1\\\\t$2\\\\t$3\\\\t$4\\\\t$5\\\\t$6\\\\t$7\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": true, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}, {\"__index__\": 1, \"find_pattern\": \"(GroupBy|collapse)\\\\(([^)]+)\\\\)\", \"replace_pattern\": \"$2\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "25f665b6-2b6a-49a3-a395-29706cd772ab",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "highest_impact_effects",
                    "output_name": "outfile",
                    "uuid": "689eb8e9-393c-4d2f-8ab6-98bcfc07892d"
                }
            ]
        },
        "15": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
            "errors": null,
            "id": 15,
            "input_connections": {
                "input_list": {
                    "id": 14,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Collapse Collection",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 1982.5,
                "top": 28.067708333333343
            },
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
            "tool_shed_repository": {
                "changeset_revision": "90981f86000f",
                "name": "collapse_collections",
                "owner": "nml",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "5.1.0",
            "type": "tool",
            "uuid": "e5459c74-11e1-45a5-beee-88c2dde61eab",
            "when": null,
            "workflow_outputs": []
        },
        "16": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
            "errors": null,
            "id": 16,
            "input_connections": {
                "input": {
                    "id": 15,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Compute",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2227.890625,
                "top": 212.38020833333331
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
            "tool_shed_repository": {
                "changeset_revision": "aff5135563c6",
                "name": "column_maker",
                "owner": "devteam",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"expressions\": [{\"__index__\": 0, \"cond\": \"c5 + '>' + c6\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}, \"new_column_name\": \"change\"}, {\"__index__\": 1, \"cond\": \"c3 + ':' + c19\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}, \"new_column_name\": \"change_with_pos\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.1",
            "type": "tool",
            "uuid": "cc8a768f-8078-4bdd-ae98-903f08619070",
            "when": null,
            "workflow_outputs": []
        },
        "17": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "errors": null,
            "id": 17,
            "input_connections": {
                "infile": {
                    "id": 16,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Replace",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2434.0625,
                "top": 80.17708333333331
            },
            "post_job_actions": {
                "RenameDatasetActionoutfile": {
                    "action_arguments": {
                        "newname": "All variants of all samples"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"EFF[*].\", \"replace_pattern\": \"\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "82276b6c-5c6e-49eb-8ee5-46041c273d30",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "all_variants_all_samples",
                    "output_name": "outfile",
                    "uuid": "708f0b5e-2bc0-4a08-96e2-d590517c7ac9"
                }
            ]
        },
        "18": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 18,
            "input_connections": {
                "in_file": {
                    "id": 17,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2685.328125,
                "top": 31.598958333333343
            },
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"20\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"collapse\", \"op_column\": \"1\"}, {\"__index__\": 4, \"op_name\": \"collapse\", \"op_column\": \"8\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "c40528c9-4fed-48c8-9c34-be2cf2c32745",
            "when": null,
            "workflow_outputs": []
        },
        "19": {
            "annotation": "",
            "content_id": "Filter1",
            "errors": null,
            "id": 19,
            "input_connections": {
                "input": {
                    "id": 17,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Filter",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2678.125,
                "top": 244.73958333333331
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "Filter1",
            "tool_state": "{\"cond\": \"c4=='PASS' or c4=='.'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.1.1",
            "type": "tool",
            "uuid": "c02e3958-04f4-499e-b78e-f304e0fdaeed",
            "when": null,
            "workflow_outputs": []
        },
        "20": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 20,
            "input_connections": {
                "in_file": {
                    "id": 17,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2969.03125,
                "top": 441.66145833333337
            },
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file"
                },
                "RenameDatasetActionout_file": {
                    "action_arguments": {
                        "newname": "Cross-sample variant stats (Datamash)"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"3\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"countunique\", \"op_column\": \"19\"}, {\"__index__\": 4, \"op_name\": \"countunique\", \"op_column\": \"13\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "a9af0104-3e05-48cb-9650-36f58d174cdf",
            "when": null,
            "workflow_outputs": []
        },
        "21": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "errors": null,
            "id": 21,
            "input_connections": {
                "infile1": {
                    "id": 19,
                    "output_name": "out_file1"
                },
                "infile2": {
                    "id": 18,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Join",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2926.71875,
                "top": 51.98958333333334
            },
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "output"
                },
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "Filtered variants of all samples with stats"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "7e27aac8-1d1e-4d82-88e3-59c4cd61baeb",
            "when": null,
            "workflow_outputs": []
        },
        "22": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 22,
            "input_connections": {
                "in_file": {
                    "id": 19,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2935.140625,
                "top": 312.1458333333333
            },
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"3\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "fac0bae2-3415-4aa3-a5f5-7950ea411d98",
            "when": null,
            "workflow_outputs": []
        },
        "23": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 23,
            "input_connections": {
                "in_file": {
                    "id": 19,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2900.640625,
                "top": 646.4114583333334
            },
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"20\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "90b934e8-ba30-49aa-9fa4-a371fdf71285",
            "when": null,
            "workflow_outputs": []
        },
        "24": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "errors": null,
            "id": 24,
            "input_connections": {
                "in_file": {
                    "id": 21,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Datamash",
            "outputs": [
                {
                    "name": "out_file",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3170.828125,
                "top": 15.098958333333343
            },
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "4c07ddedc198",
                "name": "datamash_ops",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"grouping\": \"1\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"unique\", \"op_column\": \"2\"}], \"print_full_line\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.8+galaxy0",
            "type": "tool",
            "uuid": "5ba44453-dabf-420f-a49e-2918eae031d3",
            "when": null,
            "workflow_outputs": []
        },
        "25": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "errors": null,
            "id": 25,
            "input_connections": {
                "infile1": {
                    "id": 17,
                    "output_name": "outfile"
                },
                "infile2": {
                    "id": 22,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Join",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3172.890625,
                "top": 224.66145833333331
            },
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column1\": \"3\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "3927af37-c003-4fac-a8af-88ba2b656b22",
            "when": null,
            "workflow_outputs": []
        },
        "26": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "errors": null,
            "id": 26,
            "input_connections": {
                "infile1": {
                    "id": 16,
                    "output_name": "out_file1"
                },
                "infile2": {
                    "id": 23,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Join",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3130.890625,
                "top": 592.9270833333334
            },
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "472af513-7900-41a5-b049-feb2d630ad2c",
            "when": null,
            "workflow_outputs": []
        },
        "27": {
            "annotation": "",
            "content_id": "Cut1",
            "errors": null,
            "id": 27,
            "input_connections": {
                "input": {
                    "id": 24,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Cut",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 3394.890625,
                "top": 119.89583333333331
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "Cut1",
            "tool_state": "{\"columnList\": \"c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.2",
            "type": "tool",
            "uuid": "30858ca2-a64b-4841-9bb5-5de4d38350cb",
            "when": null,
            "workflow_outputs": []
        },
        "28": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "errors": null,
            "id": 28,
            "input_connections": {
                "infile1": {
                    "id": 25,
                    "output_name": "output"
                },
                "infile2": {
                    "id": 20,
                    "output_name": "out_file"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Join",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3390.921875,
                "top": 317.8177083333333
            },
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "output"
                },
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "Filtered variants of all samples with per-position stats"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "1b250a36-d3ae-415e-9764-006182096a60",
            "when": null,
            "workflow_outputs": []
        },
        "29": {
            "annotation": "",
            "content_id": "Cut1",
            "errors": null,
            "id": 29,
            "input_connections": {
                "input": {
                    "id": 26,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Cut",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 3356.359375,
                "top": 528.6770833333334
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "Cut1",
            "tool_state": "{\"columnList\": \"c2,c3,c4,c5,c6,c7,c8,c9,c11,c12,c13,c14,c15,c16,c17,c18,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.2",
            "type": "tool",
            "uuid": "65a8b0dd-4b98-4646-bee8-a89f591816fb",
            "when": null,
            "workflow_outputs": []
        },
        "30": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "errors": null,
            "id": 30,
            "input_connections": {
                "infile": {
                    "id": 27,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Replace",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3604.359375,
                "top": 19.333333333333343
            },
            "post_job_actions": {
                "HideDatasetActionoutfile": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "outfile"
                },
                "RenameDatasetActionoutfile": {
                    "action_arguments": {
                        "newname": "All variants of all samples"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"unique\\\\(Sample\\\\)\\\\tcollapse\\\\(Sample\\\\)\\\\tcollapse\\\\(AF\\\\)\", \"replace_pattern\": \"SAMPLES(above-thresholds)\\\\tSAMPLES(all)\\\\tAFs(all)\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "6116c1c6-7c7c-43fe-9c91-609c91c6ed85",
            "when": null,
            "workflow_outputs": []
        },
        "31": {
            "annotation": "",
            "content_id": "Cut1",
            "errors": null,
            "id": 31,
            "input_connections": {
                "input": {
                    "id": 28,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Cut",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 3608.171875,
                "top": 344.31770833333337
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "Cut1",
            "tool_state": "{\"columnList\": \"c2,c1,c4,c5,c6,c7,c8,c9,c11,c10,c12,c13,c14,c15,c16,c17,c18,c23,c24,c25,c26,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.2",
            "type": "tool",
            "uuid": "a925b191-2cbc-4f45-b4cf-bbc25ba823d8",
            "when": null,
            "workflow_outputs": []
        },
        "32": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
            "errors": null,
            "id": 32,
            "input_connections": {
                "split_parms|input": {
                    "id": 29,
                    "output_name": "out_file1"
                }
            },
            "inputs": [
                {
                    "description": "runtime parameter for tool Split file",
                    "name": "split_parms"
                }
            ],
            "label": null,
            "name": "Split file",
            "outputs": [
                {
                    "name": "list_output_tab",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3579.625,
                "top": 528.8489583333334
            },
            "post_job_actions": {
                "RenameDatasetActionlist_output_tab": {
                    "action_arguments": {
                        "newname": "Per-sample variants for plotting"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "list_output_tab"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
            "tool_shed_repository": {
                "changeset_revision": "2dae863c8f42",
                "name": "split_file_to_collection",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"1\", \"split_by\": {\"select_split_by\": \"col\", \"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\", \"sub_regex\": \"\\\\1\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.5.2",
            "type": "tool",
            "uuid": "9f938b6a-e7fb-4509-9c15-271c475092aa",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "variants_for_plotting",
                    "output_name": "list_output_tab",
                    "uuid": "6bed4a2c-611a-4dd7-92bd-df5f07f0b581"
                }
            ]
        },
        "33": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1",
            "errors": null,
            "id": 33,
            "input_connections": {
                "infile": {
                    "id": 30,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Sort",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3826.890625,
                "top": 120.89583333333331
            },
            "post_job_actions": {
                "RenameDatasetActionoutfile": {
                    "action_arguments": {
                        "newname": "Combined Variant Report by Variant"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "0b2f751b-03c6-4302-9060-16856bb4157c",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "by_variant_report",
                    "output_name": "outfile",
                    "uuid": "bbb19b95-70e3-43fb-baae-525f752b86e9"
                }
            ]
        },
        "34": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1",
            "errors": null,
            "id": 34,
            "input_connections": {
                "infile": {
                    "id": 31,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Sort",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 3830.6875,
                "top": 330.55208333333337
            },
            "post_job_actions": {
                "RenameDatasetActionoutfile": {
                    "action_arguments": {
                        "newname": "Combined Variant Report by Sample"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1",
            "tool_shed_repository": {
                "changeset_revision": "86755160afbf",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "9.3+galaxy1",
            "type": "tool",
            "uuid": "e55320de-be51-4fa5-908e-76c03de24a77",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "combined_variant_report",
                    "output_name": "outfile",
                    "uuid": "3211bebc-9cdd-417b-b96d-d10cae6fd310"
                }
            ]
        },
        "35": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3",
            "errors": null,
            "id": 35,
            "input_connections": {
                "clustering|nclust": {
                    "id": 5,
                    "output_name": "output"
                },
                "sinputs": {
                    "id": 32,
                    "output_name": "list_output_tab"
                }
            },
            "inputs": [
                {
                    "description": "runtime parameter for tool Variant Frequency Plot",
                    "name": "clustering"
                }
            ],
            "label": null,
            "name": "Variant Frequency Plot",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "pdf"
                }
            ],
            "position": {
                "left": 3821.671875,
                "top": 596.9895833333334
            },
            "post_job_actions": {},
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3",
            "tool_shed_repository": {
                "changeset_revision": "3d0adeee3f2b",
                "name": "snpfreqplot",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"advanced\": {\"output_type\": \"svg\", \"ratio\": \"0.67\", \"color\": \"Set3\"}, \"clustering\": {\"do\": \"TRUE\", \"__current_case__\": 0, \"nclust\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"ward.D2\"}, \"sinputs\": {\"__class__\": \"ConnectedValue\"}, \"varfreq\": \"0.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0+galaxy3",
            "type": "tool",
            "uuid": "583b8d59-2cc0-468e-a0b7-3b1a788c7613",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "variant_frequency_plot",
                    "output_name": "outfile",
                    "uuid": "986f1d1a-02c0-4d91-9f6e-a09a088732ee"
                }
            ]
        }
    },
    "tags": [
        "COVID-19",
        "covid19.galaxyproject.org"
    ],
    "uuid": "b08c744d-7c61-4b58-ac5f-4b5886c3c643"
}