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

Changeset 0:780ad1e582e1 (2015-11-12)
Next changeset 1:95efdc025a48 (2015-11-12)
Commit message:
Uploaded
added:
Galaxy-Workflow-creation_workflow_gandalf_2.0.ga
Galaxy-Workflow-workflow_gandalf_3.0.ga
repository_dependencies.xml
b
diff -r 000000000000 -r 780ad1e582e1 Galaxy-Workflow-creation_workflow_gandalf_2.0.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Thu Nov 12 07:38:20 2015 -0500
[
b'@@ -0,0 +1,384 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "creation workflow gandalf 2.0", \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": 288, \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": 288, \n+                "top": 285\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": 288, \n+                "top": 370\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+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "name": "mdust", \n+            "outputs": [\n+                {\n+                    "name": "output_masked_fasta", \n+                    "type": "fasta"\n+                }, \n+                {\n+                    "name": "output_tab", \n+                    "type": "tabular"\n+                }, \n+                {\n+                    "name": "output_bed", \n+                    "type": "bed"\n+                }\n+            ], \n+            "position": {\n+                "left": 571, \n+                "top": 394\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionoutput_bed": {\n+                    "action_arguments": {\n+                        "newname": "#{input_file | basename}.bed"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "output_bed"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", \n+            "tool_state": "{\\"cutoff\\": \\"\\\\\\"28\\\\\\"\\", \\"input_file\\": \\"null\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"wsize\\": \\"\\\\\\"3\\\\\\"\\", \\"output_type\\": \\"{\\\\\\"output_type_selector\\\\\\": \\\\\\"bed\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"masking_letter\\": \\"{\\\\\\"masking_letter_selector\\\\\\": \\\\\\"N\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\'..b'\\\\"False\\\\\\", \\\\\\"population_model\\\\\\": {\\\\\\"population_model_selector\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"reference_allele\\\\\\": {\\\\\\"reference_allele_selector\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"optional_inputs\\\\\\": {\\\\\\"A\\\\\\": null, \\\\\\"output_trace_option\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"populations\\\\\\": null, \\\\\\"optional_inputs_selector\\\\\\": \\\\\\"True\\\\\\", \\\\\\"input_variant_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_selector\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 1}}\\", \\"reference_source\\": \\"{\\\\\\"ref_file\\\\\\": null, \\\\\\"reference_source_selector\\\\\\": \\\\\\"history\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"target_limit_type\\": \\"{\\\\\\"target_limit_type_selector\\\\\\": \\\\\\"do_not_limit\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+            "tool_version": "0.5", \n+            "type": "tool", \n+            "user_outputs": []\n+        }, \n+        "9": {\n+            "annotation": "", \n+            "id": 9, \n+            "input_connections": {\n+                "BedFile_List|BedFiles_0|inputBed": {\n+                    "id": 3, \n+                    "output_name": "output_bed"\n+                }, \n+                "inputVCF": {\n+                    "id": 8, \n+                    "output_name": "output_vcf_firstBAM"\n+                }\n+            }, \n+            "inputs": [], \n+            "name": "VCFFiltering", \n+            "outputs": [\n+                {\n+                    "name": "outputVCF", \n+                    "type": "vcf"\n+                }, \n+                {\n+                    "name": "output_html", \n+                    "type": "html"\n+                }\n+            ], \n+            "position": {\n+                "left": 1904, \n+                "top": 265\n+            }, \n+            "post_job_actions": {\n+                "RenameDatasetActionoutputVCF": {\n+                    "action_arguments": {\n+                        "newname": "#{inputVCF | basename}.filteredVCF"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "outputVCF"\n+                }, \n+                "RenameDatasetActionoutput_html": {\n+                    "action_arguments": {\n+                        "newname": "#{inputVCF | basename}.VCFFiltering.graphs"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "output_html"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", \n+            "tool_state": "{\\"inputVCF\\": \\"null\\", \\"BedFile_List\\": \\"{\\\\\\"BedFiles\\\\\\": [{\\\\\\"__index__\\\\\\": 0, \\\\\\"inputBed\\\\\\": null}], \\\\\\"is_BedFile\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"AF\\": \\"\\\\\\"0.9\\\\\\"\\", \\"__page__\\": 0, \\"DP_auto\\": \\"{\\\\\\"is_DP_auto\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"__rerun_remap_job_id__\\": null, \\"AN\\": \\"\\\\\\"2\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+            "tool_version": "0.01", \n+            "type": "tool", \n+            "user_outputs": []\n+        }\n+    }, \n+    "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r 780ad1e582e1 Galaxy-Workflow-workflow_gandalf_3.0.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-workflow_gandalf_3.0.ga Thu Nov 12 07:38:20 2015 -0500
[
b'@@ -0,0 +1,993 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "workflow gandalf 3.0", \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": 258, \n+                "top": 260\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": 258, \n+                "top": 352\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": 252, \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+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 241, \n+                "top": 520\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+        "4": {\n+            "annotation": "", \n+            "id": 4, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 245, \n+                "top": 605\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+        "5": {\n+            "annotation": "", \n+            "id": 5, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 4, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "name": "mdust", \n+            "outputs": [\n+                {\n+                    "n'..b'd": 4, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "name": "VCFStorage", \n+            "outputs": [\n+                {\n+                    "name": "outputVCFStorage", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 2067, \n+                "top": 260\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionoutputVCFStorage": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "outputVCFStorage"\n+                }, \n+                "RenameDatasetActionoutputVCFStorage": {\n+                    "action_arguments": {\n+                        "newname": "#{inputFasta | basename}.matrix"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "outputVCFStorage"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", \n+            "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"VCFFile\\": \\"[{\\\\\\"strainName\\\\\\": \\\\\\"strain1\\\\\\", \\\\\\"__index__\\\\\\": 0, \\\\\\"inputStrainVCF\\\\\\": null}, {\\\\\\"strainName\\\\\\": \\\\\\"strain2\\\\\\", \\\\\\"__index__\\\\\\": 1, \\\\\\"inputStrainVCF\\\\\\": null}]\\", \\"inputFasta\\": \\"null\\"}", \n+            "tool_version": "0.01", \n+            "type": "tool", \n+            "user_outputs": []\n+        }, \n+        "20": {\n+            "annotation": "", \n+            "id": 20, \n+            "input_connections": {\n+                "inputTabular": {\n+                    "id": 19, \n+                    "output_name": "outputVCFStorage"\n+                }\n+            }, \n+            "inputs": [], \n+            "name": "VCFCarto", \n+            "outputs": [\n+                {\n+                    "name": "outputVCFCarto", \n+                    "type": "tabular"\n+                }, \n+                {\n+                    "name": "output_html", \n+                    "type": "html"\n+                }, \n+                {\n+                    "name": "output_bed", \n+                    "type": "bed"\n+                }\n+            ], \n+            "position": {\n+                "left": 2387, \n+                "top": 260\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActionoutput_bed": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_bed"\n+                }, \n+                "HideDatasetActionoutput_html": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_html"\n+                }, \n+                "RenameDatasetActionoutputVCFCarto": {\n+                    "action_arguments": {\n+                        "newname": "#{inputTabular | basename}.red"\n+                    }, \n+                    "action_type": "RenameDatasetAction", \n+                    "output_name": "outputVCFCarto"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01", \n+            "tool_state": "{\\"__page__\\": 0, \\"parentA\\": \\"\\\\\\"strain1\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"outputType\\": \\"\\\\\\"raw\\\\\\"\\", \\"parentH\\": \\"\\\\\\"strain2\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"inputTabular\\": \\"null\\"}", \n+            "tool_version": "0.01", \n+            "type": "tool", \n+            "user_outputs": []\n+        }\n+    }, \n+    "uuid": "7924e8b4-f601-4a2e-a768-203f86c4f94e"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r 780ad1e582e1 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Nov 12 07:38:20 2015 -0500
b
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<repositories description="Gandalf worflow needed repository">
+    <repository changeset_revision="d8c9597bfb09" name="bwa" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="74980f9f1ccc" name="mapqfilter" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="379fdf4c41ac" name="picard" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="3552a8d9f51c" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="af65bfb54977" name="suite_samtools_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>