diff secreted_protein_workflow.ga @ 0:3a6de5cb858d draft

Uploaded first attempt at a workflow with dependencies on the Tool Shed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/secreted_protein_workflow.ga	Mon May 06 11:11:11 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": []
+        }
+    }
+}
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