Mercurial > repos > peterjc > rxlr_venn_workflow
view rxlr_venn_workflow.ga @ 3:1a1ab2f2b5b5 draft
README file with clearer citation instructions.
author | peterjc |
---|---|
date | Mon, 19 Aug 2013 11:35:52 -0400 |
parents | 0e7c07ff11f9 |
children | 3c280e01b920 |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "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\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", "tool_version": "0.0.6", "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\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", "tool_version": "0.0.6", "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\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", "tool_version": "0.0.6", "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, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "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, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "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, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "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\", \"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}\", \"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\\\"\", \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\"}", "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\", \"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\", \"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": [] } } }