Repository 'gandalfworkflow'
hg clone https://toolshed.g2.bx.psu.edu/repos/urgi-team/gandalfworkflow

Changeset 4:9c2cbeb63ff0 (2015-11-18)
Previous changeset 3:025efd59ddd0 (2015-11-18) Next changeset 5:33391dfcfc07 (2015-11-18)
Commit message:
Uploaded
added:
Galaxy-Workflow-workflow_gandalf_1.0.ga
b
diff -r 025efd59ddd0 -r 9c2cbeb63ff0 Galaxy-Workflow-workflow_gandalf_1.0.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-workflow_gandalf_1.0.ga Wed Nov 18 10:03:47 2015 -0500
[
b'@@ -0,0 +1,320 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "workflow gandalf 1.0", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 467, \n+                "top": 200\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "user_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 467, \n+                "top": 320\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "user_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "id": 2, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 467, \n+                "top": 440\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "user_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \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+            "name": "Map with BWA-MEM", \n+            "outputs": [\n+                {\n+                    "name": "bam_output", \n+                    "type": "bam"\n+                }\n+            ], \n+            "position": {\n+                "left": 661, \n+                "top": 204\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+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"rg\\": \\"{\\\\\\"rg_selector\\\\\\": \\\\\\"do_not_set\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"fastq_input\\": \\"{\\\\\\"iset_stats\\\\\\": \\\\\\"\\\\\\", \\\\\\"fastq_input2\\\\\\": null, \\\\\\"fastq_input_selector\\\\\\": \\\\\\"paired\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"fastq_input1\\\\\\": null}\\", \\"analysis_type\\": \\"{\\\\\\"analysis_typ'..b'type\\\\\\": {\\\\\\"input_variant_type_selector\\\\\\": \\\\\\"do_not_provide\\\\\\", \\\\\\"__current_case__\\\\\\": 0}, \\\\\\"report_monomorphic\\\\\\": \\\\\\"True\\\\\\", \\\\\\"observation_bias\\\\\\": null, \\\\\\"contamination_estimates\\\\\\": null, \\\\\\"samples\\\\\\": null, \\\\\\"output_failed_alleles_option\\\\\\": \\\\\\"False\\\\\\", \\\\\\"haplotype_basis_alleles\\\\\\": null}, \\\\\\"__current_case__\\\\\\": 0, \\\\\\"population_mappability_priors\\\\\\": {\\\\\\"population_mappability_priors_selector\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"input_filters\\\\\\": {\\\\\\"input_filters_selector\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"algorithmic_features\\\\\\": {\\\\\\"algorithmic_features_select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