view rxlr_venn_workflow.ga @ 5:4726b640f221 draft default tip

Uploaded revision to update the citation

{
    "a_galaxy_workflow": "true", 
    "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2014).", 
    "format-version": "0.1", 
    "name": "3 RXLR methods, Venn Diagram, overlap FASTA", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Input Dataset"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 363
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Input Dataset\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {
                "fasta_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "RXLR Motifs", 
            "outputs": [
                {
                    "name": "tabular_file", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 420, 
                "top": 363
            }, 
            "post_job_actions": {
                "HideDatasetActiontabular_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "fasta_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "RXLR Motifs", 
            "outputs": [
                {
                    "name": "tabular_file", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 420, 
                "top": 483
            }, 
            "post_job_actions": {
                "HideDatasetActiontabular_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "fasta_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "RXLR Motifs", 
            "outputs": [
                {
                    "name": "tabular_file", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 420, 
                "top": 603
            }, 
            "post_job_actions": {
                "HideDatasetActiontabular_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 1, 
                    "output_name": "tabular_file"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 640, 
                "top": 363
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }, 
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Positive Whisson et al. (2007) results"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "input": {
                    "id": 2, 
                    "output_name": "tabular_file"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 640, 
                "top": 483
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }, 
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Positive Win et al. (2007) results"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "input": {
                    "id": 3, 
                    "output_name": "tabular_file"
                }
            }, 
            "inputs": [], 
            "name": "Filter", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 640, 
                "top": 603
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }, 
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Positive Bhattacharjee et al. (2006) results"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "input_file": {
                    "id": 0, 
                    "output_name": "output"
                }, 
                "input_tabular": {
                    "id": 4, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter sequences by ID", 
            "outputs": [
                {
                    "name": "output_pos", 
                    "type": "fasta"
                }, 
                {
                    "name": "output_neg", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 944, 
                "top": 753
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput_neg": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_neg"
                }, 
                "HideDatasetActionoutput_pos": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_pos"
                }, 
                "RenameDatasetActionoutput_pos": {
                    "action_arguments": {
                        "newname": "Positive Whisson et al. (2007) results"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "sets_0|set": {
                    "id": 4, 
                    "output_name": "out_file1"
                }, 
                "sets_1|set": {
                    "id": 5, 
                    "output_name": "out_file1"
                }, 
                "sets_2|set": {
                    "id": 6, 
                    "output_name": "out_file1"
                }, 
                "universe|main": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Venn Diagram", 
            "outputs": [
                {
                    "name": "PDF", 
                    "type": "pdf"
                }
            ], 
            "position": {
                "left": 1086, 
                "top": 200
            }, 
            "post_job_actions": {
                "RenameDatasetActionPDF": {
                    "action_arguments": {
                        "newname": "Venn Diagram comparing RXLR predictions"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "PDF"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "venn_list", 
            "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "0.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "", 
            "id": 9, 
            "input_connections": {
                "input_file": {
                    "id": 7, 
                    "output_name": "output_pos"
                }, 
                "input_tabular": {
                    "id": 5, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter sequences by ID", 
            "outputs": [
                {
                    "name": "output_pos", 
                    "type": "fasta"
                }, 
                {
                    "name": "output_neg", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1321, 
                "top": 621
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput_neg": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_neg"
                }, 
                "HideDatasetActionoutput_pos": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_pos"
                }, 
                "RenameDatasetActionoutput_pos": {
                    "action_arguments": {
                        "newname": "Positive Whisson et al. (2007) and Win et al. (2007) results"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "", 
            "id": 10, 
            "input_connections": {
                "input_file": {
                    "id": 9, 
                    "output_name": "output_pos"
                }, 
                "input_tabular": {
                    "id": 6, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Filter sequences by ID", 
            "outputs": [
                {
                    "name": "output_pos", 
                    "type": "fasta"
                }, 
                {
                    "name": "output_neg", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1641, 
                "top": 391
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput_neg": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_neg"
                }, 
                "RenameDatasetActionoutput_pos": {
                    "action_arguments": {
                        "newname": "RXLR by all 3 methods"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}