{
    "a_galaxy_workflow": "true",
    "annotation": "16S Microbial Analysis with mothur (short)",
    "format-version": "0.1",
    "license": "MIT",
    "creator": [
        {
            "class": "Person",
            "identifier": "https://orcid.org/0000-0003-3803-468X",
            "name": "Saskia Hiltemann"
        }
    ],
    "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
    "steps": {
        "0": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "Contigs"
                }
            ],
            "label": "Contigs",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "bottom": 239.8000030517578,
                "height": 61.80000305175781,
                "left": 313,
                "right": 513,
                "top": 178,
                "width": 200,
                "x": 313,
                "y": 178
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "575ac02e-83e2-4b10-88af-6016b2ad0117",
            "workflow_outputs": []
        },
        "1": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "Groups"
                }
            ],
            "label": "Groups",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "bottom": 570.8000030517578,
                "height": 61.80000305175781,
                "left": 323,
                "right": 523,
                "top": 509,
                "width": 200,
                "x": 323,
                "y": 509
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "f6d83f4e-630a-4022-b300-e1a953c1b737",
            "workflow_outputs": []
        },
        "2": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
            "errors": null,
            "id": 2,
            "input_connections": {
                "fasta": {
                    "id": 0,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Summary.seqs",
            "outputs": [
                {
                    "name": "logfile",
                    "type": "txt"
                },
                {
                    "name": "out_summary",
                    "type": "mothur.summary"
                }
            ],
            "position": {
                "bottom": 361.5,
                "height": 266,
                "left": 631,
                "right": 831,
                "top": 95.5,
                "width": 200,
                "x": 631,
                "y": 95.5
            },
            "post_job_actions": {
                "HideDatasetActionout_summary": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_summary"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
            "tool_shed_repository": {
                "changeset_revision": "609770e516fa",
                "name": "mothur_summary_seqs",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.39.5.0",
            "type": "tool",
            "uuid": "b289d19e-f8bd-4803-88a0-e41335c11d7a",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "logfile",
                    "uuid": "09eb6090-e79e-44a7-bf2b-52c217a29c8f"
                }
            ]
        },
        "3": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
            "errors": null,
            "id": 3,
            "input_connections": {
                "fasta": {
                    "id": 0,
                    "output_name": "output"
                },
                "groups": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Screen.seqs",
            "outputs": [
                {
                    "name": "fasta_out",
                    "type": "input"
                },
                {
                    "name": "bad_accnos",
                    "type": "mothur.accnos"
                },
                {
                    "name": "groups_out",
                    "type": "mothur.groups"
                },
                {
                    "name": "alignreport_out",
                    "type": "mothur.align.report"
                },
                {
                    "name": "contigsreport_out",
                    "type": "tabular"
                }
            ],
            "position": {
                "bottom": 1128.5,
                "height": 642,
                "left": 632,
                "right": 832,
                "top": 486.5,
                "width": 200,
                "x": 632,
                "y": 486.5
            },
            "post_job_actions": {
                "HideDatasetActionalignreport_out": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "alignreport_out"
                },
                "HideDatasetActioncontigsreport_out": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "contigsreport_out"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
            "tool_shed_repository": {
                "changeset_revision": "63b74bfc8052",
                "name": "mothur_screen_seqs",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__input_ext\": \"input\", \"alignrep\": {\"usealign\": \"no\", \"__current_case__\": 1}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigsrep\": {\"usecontigs\": \"no\", \"__current_case__\": 1}, \"count\": null, \"criteria\": \"-1\", \"end\": \"-1\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"groups\": {\"__class__\": \"ConnectedValue\"}, \"maxambig\": \"0\", \"maxhomop\": \"-1\", \"maxlength\": \"275\", \"minlength\": \"10\", \"names\": null, \"optimize\": null, \"qfile\": null, \"savelog\": \"false\", \"start\": \"-1\", \"summary\": null, \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.39.5.1",
            "type": "tool",
            "uuid": "ad7d2c58-0b4d-4e3c-bb46-bfb496424b12",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "groups_out",
                    "uuid": "3361a236-0e72-4844-9956-5200e2b01252"
                },
                {
                    "label": null,
                    "output_name": "fasta_out",
                    "uuid": "c70b5192-b093-40ff-a912-bb8deff20670"
                },
                {
                    "label": null,
                    "output_name": "bad_accnos",
                    "uuid": "71c67258-d5e3-4c63-ad49-d01e54cb56cf"
                }
            ]
        },
        "4": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
            "errors": null,
            "id": 4,
            "input_connections": {
                "fasta": {
                    "id": 3,
                    "output_name": "fasta_out"
                }
            },
            "inputs": [
                {
                    "description": "runtime parameter for tool Summary.seqs",
                    "name": "count"
                },
                {
                    "description": "runtime parameter for tool Summary.seqs",
                    "name": "name"
                }
            ],
            "label": null,
            "name": "Summary.seqs",
            "outputs": [
                {
                    "name": "logfile",
                    "type": "txt"
                },
                {
                    "name": "out_summary",
                    "type": "mothur.summary"
                }
            ],
            "position": {
                "bottom": 393,
                "height": 266,
                "left": 959,
                "right": 1159,
                "top": 127,
                "width": 200,
                "x": 959,
                "y": 127
            },
            "post_job_actions": {
                "HideDatasetActionout_summary": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_summary"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
            "tool_shed_repository": {
                "changeset_revision": "609770e516fa",
                "name": "mothur_summary_seqs",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.39.5.0",
            "type": "tool",
            "uuid": "f7268117-2f00-48d7-aed0-cc3e149db198",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "logfile",
                    "uuid": "b4abf87f-39ec-4d17-8e93-5a2a473dab74"
                }
            ]
        },
        "5": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
            "errors": null,
            "id": 5,
            "input_connections": {
                "fasta": {
                    "id": 3,
                    "output_name": "fasta_out"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Unique.seqs",
            "outputs": [
                {
                    "name": "out_fasta",
                    "type": "input"
                },
                {
                    "name": "out_names",
                    "type": "mothur.names"
                }
            ],
            "position": {
                "bottom": 850.1000061035156,
                "height": 235.60000610351562,
                "left": 1009,
                "right": 1209,
                "top": 614.5,
                "width": 200,
                "x": 1009,
                "y": 614.5
            },
            "post_job_actions": {},
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
            "tool_shed_repository": {
                "changeset_revision": "d466580cd706",
                "name": "mothur_unique_seqs",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"format\": \"name\", \"names\": null, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.39.5.0",
            "type": "tool",
            "uuid": "3256bd7b-b98f-4248-90ae-c5e73704f418",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "out_fasta",
                    "uuid": "10d11427-086d-47fe-aee9-ac5d1bae3191"
                },
                {
                    "label": null,
                    "output_name": "out_names",
                    "uuid": "2bde74d8-08ef-4bd6-b54f-138c0d4d365f"
                }
            ]
        },
        "6": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
            "errors": null,
            "id": 6,
            "input_connections": {
                "grouping|group": {
                    "id": 3,
                    "output_name": "groups_out"
                },
                "name": {
                    "id": 5,
                    "output_name": "out_names"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Count.seqs",
            "outputs": [
                {
                    "name": "seq_count",
                    "type": "mothur.count_table"
                }
            ],
            "position": {
                "bottom": 556.6999969482422,
                "height": 205.1999969482422,
                "left": 1292,
                "right": 1492,
                "top": 351.5,
                "width": 200,
                "x": 1292,
                "y": 351.5
            },
            "post_job_actions": {},
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
            "tool_shed_repository": {
                "changeset_revision": "7a6f9c899221",
                "name": "mothur_count_seqs",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": {\"use\": \"yes\", \"__current_case__\": 0, \"group\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null}, \"name\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.39.5.0",
            "type": "tool",
            "uuid": "51efceca-f05a-4f3f-af6b-693a14b26048",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "seq_count",
                    "uuid": "5ffc59a1-8b3f-4b09-982d-332411f16919"
                }
            ]
        }
    },
    "tags": [
        "microbiome"
    ],
    "uuid": "ecab68d9-136b-4f05-8304-6f67f7addd24",
    "version": 4
}