Mercurial > repos > earlhaminst > geneseqtofamily

view finding_orphan_genes.ga @ 6:266800d51605 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
author earlhaminst
date Thu, 10 Jun 2021 16:18:59 +0000
parents 267a94f068d7
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Orphan genes", 
    "steps": {
        "0": {
            "annotation": "Output file from blast_parser of GeneSeqToFamily", 
            "content_id": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Output file from blast_parser of GeneSeqToFamily", 
                    "name": "blast_parser data"
                }
            ], 
            "label": "blast_parser data", 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 199.9375, 
                "top": 276.4375
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"blast_parser data\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "f8f73cb1-7472-44e6-9bd6-40dd0f2103d0", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "197d2b5b-2790-4eb8-be7d-f2ee15165b2a"
                }
            ]
        }, 
        "1": {
            "annotation": "Same CDS, used to run BLASTP in GeneSeqToFamily", 
            "content_id": null, 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Same CDS, used to run BLASTP in GeneSeqToFamily", 
                    "name": "CDS"
                }
            ], 
            "label": "CDS", 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 195.921875, 
                "top": 553.359375
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"CDS\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "2856205c-2a2b-4f2a-a177-2bfc78352840", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "5e46019a-f8fb-4507-8206-2402d8088ca5"
                }
            ]
        }, 
        "2": {
            "annotation": "List of IDs discarded from hcluster_sg results", 
            "content_id": null, 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "List of IDs discarded from hcluster_sg results", 
                    "name": "hcluster_sg discarded"
                }
            ], 
            "label": "hcluster_sg discarded", 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 191, 
                "top": 697
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"hcluster_sg discarded\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "3866a37f-3309-4c5d-8ed9-bb7c21d25d8a", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "f9fe709d-8a1b-44b0-9989-688af44b16ad"
                }
            ]
        }, 
        "3": {
            "annotation": "", 
            "content_id": "Cut1", 
            "id": 3, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Cut", 
                    "name": "input"
                }
            ], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 429.953125, 
                "top": 276.4375
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.2", 
            "type": "tool", 
            "uuid": "3d809485-291c-4858-ade6-2f465bf667f0", 
            "workflow_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool FASTA-to-Tabular", 
                    "name": "input"
                }
            ], 
            "label": null, 
            "name": "FASTA-to-Tabular", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 429.953125, 
                "top": 389.4375
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", 
            "tool_shed_repository": {
                "changeset_revision": "7e801ab2b70e", 
                "name": "fasta_to_tabular", 
                "owner": "devteam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "uuid": "614def54-f941-49a4-950c-69f651e6b35f", 
            "workflow_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", 
            "id": 5, 
            "input_connections": {
                "infile": {
                    "id": 3, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Unique", 
                    "name": "infile"
                }
            ], 
            "label": null, 
            "name": "Unique", 
            "outputs": [
                {
                    "name": "outfile", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 659.984375, 
                "top": 199.9375
            }, 
            "post_job_actions": {
                "HideDatasetActionoutfile": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "outfile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", 
            "tool_shed_repository": {
                "changeset_revision": "20344ce0c811", 
                "name": "text_processing", 
                "owner": "bgruening", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "uuid": "55da94d2-b1d9-46ed-9668-db9b7f19a5bb", 
            "workflow_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "content_id": "Cut1", 
            "id": 6, 
            "input_connections": {
                "input": {
                    "id": 4, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Cut", 
                    "name": "input"
                }
            ], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 675.953125, 
                "top": 389.4375
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.2", 
            "type": "tool", 
            "uuid": "5bae54ed-b8c8-432c-9980-422d0f678be3", 
            "workflow_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "content_id": "Cut1", 
            "id": 7, 
            "input_connections": {
                "input": {
                    "id": 5, 
                    "output_name": "outfile"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Cut", 
                    "name": "input"
                }
            ], 
            "label": null, 
            "name": "Cut", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 917.9375, 
                "top": 198.46875
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Cut1", 
            "tool_state": "{\"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"U\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.0.2", 
            "type": "tool", 
            "uuid": "d6dc6ba2-efc0-4e90-8562-4739c4f41fab", 
            "workflow_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "content_id": "comp1", 
            "id": 8, 
            "input_connections": {
                "input1": {
                    "id": 6, 
                    "output_name": "out_file1"
                }, 
                "input2": {
                    "id": 7, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Compare two Datasets", 
                    "name": "input2"
                }, 
                {
                    "description": "runtime parameter for tool Compare two Datasets", 
                    "name": "input1"
                }
            ], 
            "label": null, 
            "name": "Compare two Datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1123.9375, 
                "top": 363.453125
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "comp1", 
            "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"field2\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"field1\": \"\\\"1\\\"\", \"mode\": \"\\\"V\\\"\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.2", 
            "type": "tool", 
            "uuid": "7c71fbae-828d-4c99-8f7b-fe1a90b27626", 
            "workflow_outputs": []
        }, 
        "9": {
            "annotation": "", 
            "content_id": "cat1", 
            "id": 9, 
            "input_connections": {
                "input1": {
                    "id": 8, 
                    "output_name": "out_file1"
                }, 
                "queries_0|input2": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Concatenate datasets", 
                    "name": "input1"
                }
            ], 
            "label": null, 
            "name": "Concatenate datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1130.5, 
                "top": 686
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "cat1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"queries\": \"[{\\\"input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__index__\\\": 0}]\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "uuid": "8a1e29ca-8dec-4143-9db1-f38f820b0e9a", 
            "workflow_outputs": []
        }, 
        "10": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 
            "id": 10, 
            "input_connections": {
                "identifiers": {
                    "id": 9, 
                    "output_name": "out_file1"
                }, 
                "input": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Filter by FASTA IDs", 
                    "name": "input"
                }, 
                {
                    "description": "runtime parameter for tool Filter by FASTA IDs", 
                    "name": "identifiers"
                }
            ], 
            "label": null, 
            "name": "Filter by FASTA IDs", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1392.921875, 
                "top": 550.453125
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 
            "tool_shed_repository": {
                "changeset_revision": "8d15aebf55fd", 
                "name": "filter_by_fasta_ids", 
                "owner": "galaxyp", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"identifiers\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dedup\": \"\\\"true\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0", 
            "type": "tool", 
            "uuid": "5f5fb6ac-f026-41bc-a89c-2d1d882ece85", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "56824bb4-df6b-4ebc-8c89-c6731b5d76f1"
                }
            ]
        }
    }, 
    "uuid": "cf6b9210-2ed8-46b1-920e-ac6303ed44d5"
}