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

Changeset 6:7557b71a92e7 (2015-11-25)
Previous changeset 5:33391dfcfc07 (2015-11-18) Next changeset 7:a6b557df86db (2015-12-15)
Commit message:
Uploaded
added:
Galaxy-Workflow-workflow_gandalf_1_set.ga
Galaxy-Workflow-workflow_gandalf_2_sets.ga
removed:
Galaxy-Workflow-creation_workflow_gandalf_2.0.ga
Galaxy-Workflow-workflow_gandalf_1.0.ga
Galaxy-Workflow-workflow_gandalf_3.0.ga
b
diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-creation_workflow_gandalf_2.0.ga
--- a/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Wed Nov 18 10:54:56 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,384 +0,0 @@\n-{\n-    "a_galaxy_workflow": "true", \n-    "annotation": "", \n-    "format-version": "0.1", \n-    "name": "workflow gandalf 1 set", \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'case__\\\\\\": 1}, \\\\\\"O\\\\\\": \\\\\\"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'
b
diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_1.0.ga
--- a/Galaxy-Workflow-workflow_gandalf_1.0.ga Wed Nov 18 10:54:56 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,320 +0,0 @@\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_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": "0.4", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "7": {\n-            "annotation": "", \n-            "id": 7, \n-            "input_connections": {\n-                "input1": {\n-                    "id": 5, \n-                    "output_name": "outFile"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "flagstat", \n-            "outputs": [\n-                {\n-                    "name": "output1", \n-                    "type": "txt"\n-                }\n-            ], \n-            "position": {\n-                "left": 1395, \n-                "top": 208\n-            }, \n-            "post_job_actions": {}, \n-            "tool_errors": null, \n-            "tool_id": "samtools_flagstat", \n-            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n-            "tool_version": "1.0.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "8": {\n-            "annotation": "", \n-            "id": 8, \n-            "input_connections": {\n-                "inputVCF": {\n-                    "id": 6, \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": 1714, \n-                "top": 180\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-            }, \n-            "tool_errors": null, \n-            "tool_id": "10.0.0.125:9009/repos/urgiteam/vcfgandalftools/VCFFiltering/0.01", \n-            "tool_state": "{\\"inputVCF\\": \\"null\\", \\"BedFile_List\\": \\"{\\\\\\"is_BedFile\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"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": "1a7a40af-5624-4049-a1dd-fee31e8731ee"\n-}\n\\ No newline at end of file\n'
b
diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_1_set.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-workflow_gandalf_1_set.ga Wed Nov 25 09:34:17 2015 -0500
[
b'@@ -0,0 +1,384 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "workflow gandalf 1 set", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Reference genome"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 128, \n+                "top": 198\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Reference genome\\"}", \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": "Genome reads forward "\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 157, \n+                "top": 295\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Genome reads forward \\"}", \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": "Genome read Reverse"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 193, \n+                "top": 394\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Genome read Reverse\\"}", \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": 395\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'..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": 266\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": "58cfd654-45c2-443f-9c8c-b862c0b4ca06"\n+}\n\\ No newline at end of file\n'
b
diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_2_sets.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-workflow_gandalf_2_sets.ga Wed Nov 25 09:34:17 2015 -0500
[
b'@@ -0,0 +1,933 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "workflow gandalf 2 sets", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Reference genome"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 248, \n+                "top": 874\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"Reference genome\\"}", \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": "genome 1 reads forward"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 280, \n+                "top": 979\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"genome 1 reads forward\\"}", \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": "genome 1 reads reverse"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 288, \n+                "top": 1048\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"genome 1 reads reverse\\"}", \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": "genome 2 reads forward"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 346, \n+                "top": 1206\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"genome 2 reads forward\\"}", \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": "genome 2 reads reverse"\n+                }\n+            ], \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 344, \n+                "top": 1277\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"genome 2 reads reverse\\"}", \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": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "n'..b'd": 0, \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": 2298, \n+                "top": 593\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+        "19": {\n+            "annotation": "", \n+            "id": 19, \n+            "input_connections": {\n+                "inputTabular": {\n+                    "id": 18, \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": 2618, \n+                "top": 593\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": "f217cc60-5c89-442b-80ee-3d055e407367"\n+}\n\\ No newline at end of file\n'
b
diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_3.0.ga
--- a/Galaxy-Workflow-workflow_gandalf_3.0.ga Wed Nov 18 10:54:56 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,933 +0,0 @@\n-{\n-    "a_galaxy_workflow": "true", \n-    "annotation": "", \n-    "format-version": "0.1", \n-    "name": "workflow gandalf 2 sets", \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": 593\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": 685\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": 773\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": 853\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": 938\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-                "fastq_input|fastq_input1": {\n-                    "id": 2, \n-                    "output_name": "output"\n-                }, \n-                "fastq_input|fastq_input2": {\n-                    "id": 0, \n-                    "output_name": "output"\n- '..b'": {\n-                    "id": 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": 593\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-        "19": {\n-            "annotation": "", \n-            "id": 19, \n-            "input_connections": {\n-                "inputTabular": {\n-                    "id": 18, \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": 593\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": "359c9c1b-1771-475c-b353-1b9a0d802f18"\n-}\n'