Mercurial > repos > peterjc > secreted_protein_workflow
diff secreted_protein_workflow.ga @ 0:0ec2a079f68d draft
Uploaded v0.0.1, includes README file and dependencies.
| author | peterjc |
|---|---|
| date | Mon, 06 May 2013 11:29:15 -0400 |
| parents | |
| children | 3a0c0d1c388f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/secreted_protein_workflow.ga Mon May 06 11:29:15 2013 -0400 @@ -0,0 +1,288 @@ +{ + "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": [] + } + } +} \ No newline at end of file