Mercurial > repos > peterjc > secreted_protein_workflow
view secreted_protein_workflow.ga @ 5:5f3cc8229771 draft
Uploaded v0.0.1e with links to sample data in README
author | peterjc |
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date | Tue, 20 Aug 2013 07:37:19 -0400 |
parents | 3a6de5cb858d |
children | 36b2c2b5051e |
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{ "a_galaxy_workflow": "true", "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.", "format-version": "0.1", "name": "Find secreted proteins with TMHMM and SignalP", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 200 }, "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": [ { "description": "runtime parameter for tool SignalP 3.0", "name": "organism" } ], "name": "SignalP 3.0", "outputs": [ { "name": "tabular_file", "type": "tabular" } ], "position": { "left": 240, "top": 341 }, "post_job_actions": { "HideDatasetActiontabular_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "tabular_file" } }, "tool_errors": null, "tool_id": "signalp3", "tool_state": "{\"organism\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"truncate\": \"\\\"60\\\"\", \"__page__\": 0}", "tool_version": "0.0.8", "type": "tool", "user_outputs": [] }, "2": { "annotation": "Select proteins with predicted signal peptide (SignalP NN D-Score or HMM)", "id": 2, "input_connections": { "input": { "id": 1, "output_name": "tabular_file" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 323, "top": 528 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Filtered SignalP results" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c14=='Y' or c15=='S'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "3": { "annotation": "Select those sequences with signal peptides.", "id": 3, "input_connections": { "input_file": { "id": 0, "output_name": "output" }, "input_tabular": { "id": 2, "output_name": "out_file1" } }, "inputs": [], "name": "Filter sequences by ID", "outputs": [ { "name": "output_pos", "type": "fasta" }, { "name": "output_neg", "type": "fasta" } ], "position": { "left": 527, "top": 200 }, "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" } }, "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": "0.0.1", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "fasta_file": { "id": 3, "output_name": "output_pos" } }, "inputs": [], "name": "TMHMM 2.0", "outputs": [ { "name": "tabular_file", "type": "tabular" } ], "position": { "left": 643, "top": 443 }, "post_job_actions": { "HideDatasetActiontabular_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "tabular_file" } }, "tool_errors": null, "tool_id": "tmhmm2", "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.0.7", "type": "tool", "user_outputs": [] }, "5": { "annotation": "Select proteins with no predicted transmembrane helices.", "id": 5, "input_connections": { "input": { "id": 4, "output_name": "tabular_file" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 729, "top": 566 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Filtered TMHMM results" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c5== 0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "6": { "annotation": "Select those sequences with no transmembrane helices (from those with signal peptides).", "id": 6, "input_connections": { "input_file": { "id": 3, "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": 893, "top": 281 }, "post_job_actions": { "HideDatasetActionoutput_neg": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_neg" }, "RenameDatasetActionoutput_pos": { "action_arguments": { "newname": "Secreted proteins" }, "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": "0.0.1", "type": "tool", "user_outputs": [] } } }