# HG changeset patch
# User john-mccallum
# Date 1350604027 14400
# Node ID be070a68521ebdd66d89da402a30c2fd634b8d20
# Parent  402c3f0fe8074add8c39092c7d211abb4833ecc3
Uploaded workflow from vcf file to CAPS

diff -r 402c3f0fe807 -r be070a68521e Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga	Thu Oct 18 19:47:07 2012 -0400
@@ -0,0 +1,273 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "CAPS Marker Design from VCF", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Multi fasta Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 214, 
+                "top": 225
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Multi fasta Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input VCF  Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 174, 
+                "top": 592
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input VCF  Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "inputVcf": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Convert vcf to gff", 
+            "outputs": [
+                {
+                    "name": "outputfile", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 460.99998474121094, 
+                "top": 568
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/vcf2gff_1/1.0.0", 
+            "tool_state": "{\"inputVcf\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "Detect resitriction polymorphisms", 
+            "id": 3, 
+            "input_connections": {
+                "inputFasta": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "inputSNPGff3File": {
+                    "id": 2, 
+                    "output_name": "outputfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "CAPS Detection", 
+            "outputs": [
+                {
+                    "name": "outputfile", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
+                "left": 646.99998474121094, 
+                "top": 382
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0", 
+            "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "get feature ID column", 
+            "id": 4, 
+            "input_connections": {
+                "input": {
+                    "id": 3, 
+                    "output_name": "outputfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 892, 
+                "top": 415
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "inputSNPfile": {
+                    "id": 2, 
+                    "output_name": "outputfile"
+                }, 
+                "inputTargetfile": {
+                    "id": 4, 
+                    "output_name": "out_file1"
+                }, 
+                "inputfastaFile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Design primers to features", 
+                    "name": "min_size"
+                }, 
+                {
+                    "description": "runtime parameter for tool Design primers to features", 
+                    "name": "max_size"
+                }
+            ], 
+            "name": "Design primers to features", 
+            "outputs": [
+                {
+                    "name": "primer_outputfile", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1186, 
+                "top": 382
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionprimer_outputfile": {
+                    "action_arguments": {
+                        "newname": "PrimerPairs"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "primer_outputfile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"inputTargetfile\": \"null\", \"inputfastaFile\": \"null\", \"min_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputSNPfile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"max_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input": {
+                    "id": 5, 
+                    "output_name": "primer_outputfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Select", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1406, 
+                "top": 382
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionout_file1": {
+                    "action_arguments": {
+                        "newname": "SuccessfulDesignSets"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "Grep1", 
+            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"NONE\\\"\"}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 6, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Unique", 
+            "outputs": [
+                {
+                    "name": "outputfile", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1625.9999389648438, 
+                "top": 382
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputfile": {
+                    "action_arguments": {
+                        "newname": "UniquePrimerSets"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputfile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
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