changeset 0:8b008a3c3ccb

Uploaded
author jjohnson
date Tue, 12 Mar 2013 14:59:40 -0400
parents
children 6e49aa2461bd
files Galaxy-Workflow-MMuFF_v1.2.ga
diffstat 1 files changed, 963 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-MMuFF_v1.2.ga	Tue Mar 12 14:59:40 2013 -0400
@@ -0,0 +1,963 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "MMuFF_v1.2", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Forward reads fastq"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 244, 
+                "top": 313
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Forward reads fastq\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reverse reads fastq"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 242, 
+                "top": 410
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reverse reads fastq\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "dbSNP.vcf", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "dbSNP.vcf", 
+                    "name": "VCF file of known variants (dbSNP)"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 4063, 
+                "top": 532
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "These are locations other than those in dbSNP.  The ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y) even if it is a bogus value at position 1", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "These are locations other than those in dbSNP.  The ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y) even if it is a bogus value at position 1", 
+                    "name": "VCF file of additional known variants "
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 4388, 
+                "top": 573
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"VCF file of additional known variants \"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
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+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Groomer", 
+                    "name": "input_type"
+                }
+            ], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 510, 
+                "top": 288
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+            "post_job_actions": {}, 
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+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Groomer", 
+                    "name": "input_type"
+                }
+            ], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 505, 
+                "top": 428
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+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastq_groomer", 
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+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
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+            "annotation": "Use a GATK compatible genome reference.", 
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+            "input_connections": {
+                "input1": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }, 
+                "singlePaired|input2": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Tophat for Illumina", 
+                    "name": "refGenomeSource"
+                }
+            ], 
+            "name": "Tophat for Illumina", 
+            "outputs": [
+                {
+                    "name": "insertions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "deletions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "junctions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "accepted_hits", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 884, 
+                "top": 329
+            }, 
+            "post_job_actions": {
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+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "deletions"
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+                "HideDatasetActioninsertions": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "insertions"
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+                "HideDatasetActionjunctions": {
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+                    "action_type": "HideDatasetAction", 
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+            "type": "tool", 
+            "user_outputs": []
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+            "id": 7, 
+            "input_connections": {
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+                    "output_name": "accepted_hits"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1154, 
+                "top": 363
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
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+            }, 
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+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "flagstat", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1505, 
+                "top": 320
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+            "post_job_actions": {}, 
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+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
+            "tool_version": "1.0.0", 
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+            "user_outputs": []
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+            "id": 9, 
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+                "inputFile": {
+                    "id": 7, 
+                    "output_name": "output1"
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+            }, 
+            "inputs": [], 
+            "name": "Add or Replace Groups", 
+            "outputs": [
+                {
+                    "name": "outFile", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1506, 
+                "top": 500
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+            "post_job_actions": {}, 
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+                    "output_name": "outFile"
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+            }, 
+            "inputs": [], 
+            "name": "Paired Read Mate Fixer", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1841, 
+                "top": 372
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+            "post_job_actions": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file"
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+            "input_connections": {
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+                    "id": 10, 
+                    "output_name": "out_file"
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+            }, 
+            "inputs": [], 
+            "name": "Mark Duplicate reads", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
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+                "top": 357
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+            "post_job_actions": {}, 
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+            "type": "tool", 
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+            "annotation": "Set to same GATK compatible genome reference as tophat", 
+            "id": 12, 
+            "input_connections": {
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+                    "id": 11, 
+                    "output_name": "out_file"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Reorder SAM/BAM", 
+                    "name": "source"
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+            ], 
+            "name": "Reorder SAM/BAM", 
+            "outputs": [
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+                    "name": "outFile", 
+                    "type": "bam"
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+                "top": 323
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+            "type": "tool", 
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+                    "output_name": "outFile"
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+                    "description": "runtime parameter for tool Realigner Target Creator", 
+                    "name": "reference_source"
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+            "name": "Realigner Target Creator", 
+            "outputs": [
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+                    "name": "output_interval", 
+                    "type": "gatk_interval"
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+                {
+                    "name": "output_log", 
+                    "type": "txt"
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+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
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+                    "output_name": "outFile"
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+                    "output_name": "output_interval"
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+            }, 
+            "inputs": [
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+                    "description": "runtime parameter for tool Indel Realigner", 
+                    "name": "reference_source"
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+            ], 
+            "name": "Indel Realigner", 
+            "outputs": [
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+                    "name": "output_bam", 
+                    "type": "bam"
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+                {
+                    "name": "output_log", 
+                    "type": "txt"
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+                "top": 348
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+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
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+            "tool_errors": null, 
+            "tool_id": "gatk_indel_realigner", 
+            "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", 
+            "tool_version": "0.0.6", 
+            "type": "tool", 
+            "user_outputs": []
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+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "input_file": {
+                    "id": 14, 
+                    "output_name": "output_bam"
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+            }, 
+            "inputs": [], 
+            "name": "Mark Duplicate reads", 
+            "outputs": [
+                {
+                    "name": "out_file", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
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+            "position": {
+                "left": 3174, 
+                "top": 315
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+            "post_job_actions": {
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+                    "action_arguments": {}, 
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+                    "output_name": "html_file"
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+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file"
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+                    "id": 15, 
+                    "output_name": "out_file"
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+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MPileup", 
+                    "name": "reference_source"
+                }
+            ], 
+            "name": "MPileup", 
+            "outputs": [
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+                    "name": "output_mpileup", 
+                    "type": "pileup"
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+                {
+                    "name": "output_log", 
+                    "type": "txt"
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+}
\ No newline at end of file