# HG changeset patch
# User ulfschaefer
# Date 1462871768 14400
# Node ID 162c88041ed74be2b7c677380c27d49dc9d644d1
# Parent  cb29f95c7b885971886e3423eb0def4017c161eb
Uploaded

diff -r cb29f95c7b88 -r 162c88041ed7 Galaxy-Workflow-Phenix_workflow.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Phenix_workflow.ga	Tue May 10 05:16:08 2016 -0400
@@ -0,0 +1,219 @@
+{
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+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Phenix workflow", 
+    "steps": {
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+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference fasta"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 116
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference fasta\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "576fa42b-080a-4cc4-aff3-2f2eac3fe3b7", 
+            "workflow_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "R1 fastq"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 207, 
+                "top": 334
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"R1 fastq\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "10a74ae8-b3f1-4409-8502-f6f79a55b071", 
+            "workflow_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "R2 fastqs"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 211, 
+                "top": 462
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"R2 fastqs\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
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+            "workflow_outputs": []
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+            "id": 3, 
+            "input_connections": {
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+                    "output_name": "output"
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+                    "output_name": "output"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Map with BWA-MEM", 
+            "outputs": [
+                {
+                    "name": "bam_output", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 423.5, 
+                "top": 288
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+            "post_job_actions": {
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+                    "action_arguments": {
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+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "bam_output"
+                }
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+            "tool_errors": null, 
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+            "uuid": "e7189b5b-110c-4e8f-ae4e-a85d9e7bf8c3", 
+            "workflow_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
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+            "id": 4, 
+            "input_connections": {
+                "input_bam": {
+                    "id": 3, 
+                    "output_name": "bam_output"
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+                "ref_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "PHE MPileup", 
+            "outputs": [
+                {
+                    "name": "outvcf", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 634, 
+                "top": 126
+            }, 
+            "post_job_actions": {
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+                    "action_arguments": {
+                        "newname": "#{input_bam | basename}.vcf"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outvcf"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 
+            "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "uuid": "6f7b0596-34f3-4588-9094-04edb6848a4b", 
+            "workflow_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
+            "id": 5, 
+            "input_connections": {
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+                    "output_name": "outvcf"
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+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Filter VCF", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
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+                "top": 314
+            }, 
+            "post_job_actions": {
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+                    "action_arguments": {
+                        "newname": "#{input | basename}.filtered.vcf"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
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+            "tool_version": "1.0", 
+            "type": "tool", 
+            "uuid": "caf82bf3-cccc-47f7-9721-6ef9057173bb", 
+            "workflow_outputs": []
+        }
+    }, 
+    "uuid": "d0b49f14-3813-4724-bcee-88a3ce3fb2e8"
+}
\ No newline at end of file