Repository 'phephenix'
hg clone https://toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix

Changeset 1:162c88041ed7 (2016-05-10)
Previous changeset 0:cb29f95c7b88 (2016-05-09) Next changeset 2:79fc19ba1cbc (2016-05-10)
Commit message:
Uploaded
added:
Galaxy-Workflow-Phenix_workflow.ga
b
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
[
b'@@ -0,0 +1,219 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "Phenix workflow", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Reference fasta"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 200, \n+                "top": 116\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Reference fasta\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "576fa42b-080a-4cc4-aff3-2f2eac3fe3b7", \n+            "workflow_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "R1 fastq"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 207, \n+                "top": 334\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"R1 fastq\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "10a74ae8-b3f1-4409-8502-f6f79a55b071", \n+            "workflow_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 2, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "R2 fastqs"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 211, \n+                "top": 462\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"R2 fastqs\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "58fb33f3-4e67-4376-8b82-afab515e9be1", \n+            "workflow_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", \n+            "id": 3, \n+            "input_connections": {\n+                "fastq_input|fastq_input1": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }, \n+                "fastq_input|fastq_input2": {\n+                    "id": 2, \n+                    "output_name": "output"\n+                }, \n+                "reference_source|ref_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Map with BWA-MEM", \n+            "outputs": [\n+                {\n+                    "name": "bam_output", \n+                    "type": "bam"\n+                }\n+            ], \n+            "position": {\n+                "left": 423.5, \n+                "top": 288\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionbam_output": {\n+                    "action_arguments": {\n+                        "newname": "#{fastq_input1 | basename}.bam"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "bam_output"\n+                }\n+            }, \n+            "to'..b'_case__\\\\\\": 0}\\", \\"reference_source\\": \\"{\\\\\\"ref_file\\\\\\": null, \\\\\\"reference_source_selector\\\\\\": \\\\\\"history\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"index_a\\\\\\": \\\\\\"auto\\\\\\"}\\"}", \n+            "tool_version": "0.7.12.1", \n+            "type": "tool", \n+            "uuid": "e7189b5b-110c-4e8f-ae4e-a85d9e7bf8c3", \n+            "workflow_outputs": []\n+        }, \n+        "4": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", \n+            "id": 4, \n+            "input_connections": {\n+                "input_bam": {\n+                    "id": 3, \n+                    "output_name": "bam_output"\n+                }, \n+                "ref_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "PHE MPileup", \n+            "outputs": [\n+                {\n+                    "name": "outvcf", \n+                    "type": "vcf"\n+                }\n+            ], \n+            "position": {\n+                "left": 634, \n+                "top": 126\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionoutvcf": {\n+                    "action_arguments": {\n+                        "newname": "#{input_bam | basename}.vcf"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "outvcf"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", \n+            "tool_state": "{\\"ref_file\\": \\"null\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input_bam\\": \\"null\\"}", \n+            "tool_version": "1.0", \n+            "type": "tool", \n+            "uuid": "6f7b0596-34f3-4588-9094-04edb6848a4b", \n+            "workflow_outputs": []\n+        }, \n+        "5": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", \n+            "id": 5, \n+            "input_connections": {\n+                "input": {\n+                    "id": 4, \n+                    "output_name": "outvcf"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Filter VCF", \n+            "outputs": [\n+                {\n+                    "name": "output", \n+                    "type": "vcf"\n+                }\n+            ], \n+            "position": {\n+                "left": 747, \n+                "top": 314\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionoutput": {\n+                    "action_arguments": {\n+                        "newname": "#{input | basename}.filtered.vcf"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "output"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", \n+            "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"snp_filter\\": \\"[{\\\\\\"__index__\\\\\\": 0, \\\\\\"snp_filter_type\\\\\\": {\\\\\\"dp4_ratio\\\\\\": \\\\\\"0.9\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"snp_filter_type_selector\\\\\\": \\\\\\"dp4_ratio_option\\\\\\"}}, {\\\\\\"__index__\\\\\\": 1, \\\\\\"snp_filter_type\\\\\\": {\\\\\\"min_depth\\\\\\": \\\\\\"10\\\\\\", \\\\\\"__current_case__\\\\\\": 4, \\\\\\"snp_filter_type_selector\\\\\\": \\\\\\"min_depth_option\\\\\\"}}]\\", \\"onlygood\\": \\"\\\\\\"false\\\\\\"\\"}", \n+            "tool_version": "1.0", \n+            "type": "tool", \n+            "uuid": "caf82bf3-cccc-47f7-9721-6ef9057173bb", \n+            "workflow_outputs": []\n+        }\n+    }, \n+    "uuid": "d0b49f14-3813-4724-bcee-88a3ce3fb2e8"\n+}\n\\ No newline at end of file\n'