--- /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
@@ -0,0 +1,384 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "creation workflow gandalf 2.0", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 288, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 288, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 288, 
+                "top": 370
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mdust", 
+            "outputs": [
+                {
+                    "name": "output_masked_fasta", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "output_tab", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_bed", 
+                    "type": "bed"
+                }
+            ], 
+            "position": {
+                "left": 571, 
+                "top": 394
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput_bed": {
+                    "action_arguments": {
+                        "newname": "#{input_file | basename}.bed"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_bed"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", 
+            "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\\\"\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "fastq_input|fastq_input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "fastq_input|fastq_input2": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA-MEM", 
+            "outputs": [
+                {
+                    "name": "bam_output", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 516, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionbam_output": {
+                    "action_arguments": {
+                        "newname": "#{fastq_input1 | basename}.bam"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "bam_output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__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\\\"\"}", 
+            "tool_version": "0.4.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input1": {
+                    "id": 4, 
+                    "output_name": "bam_output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mapQfilter", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 844, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput1": {
+                    "action_arguments": {
+                        "newname": "#{input1 | basename}.filteredbam"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 5, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MarkDuplicates", 
+            "outputs": [
+                {
+                    "name": "metrics_file", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outFile", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1072, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutFile": {
+                    "action_arguments": {
+                        "newname": "#{inputFile | basename}.markedBAM"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", 
+            "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.126.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "input1": {
+                    "id": 6, 
+                    "output_name": "outFile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "flagstat", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1400, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput1": {
+                    "action_arguments": {
+                        "newname": "#{inupt1| basename}.stats"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input_bams_0|input_bam": {
+                    "id": 6, 
+                    "output_name": "outFile"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Freebayes4Workflow", 
+            "outputs": [
+                {
+                    "name": "output_vcf_default", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "output_vcf_firstBAM", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "output_vcf_rename", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "output_failed_alleles_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "output_trace", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1400, 
+                "top": 313
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", 
+            "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_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}\"}", 
+            "tool_version": "0.5", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "BedFile_List|BedFiles_0|inputBed": {
+                    "id": 3, 
+                    "output_name": "output_bed"
+                }, 
+                "inputVCF": {
+                    "id": 8, 
+                    "output_name": "output_vcf_firstBAM"
+                }
+            }, 
+            "inputs": [], 
+            "name": "VCFFiltering", 
+            "outputs": [
+                {
+                    "name": "outputVCF", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "output_html", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 1904, 
+                "top": 265
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputVCF": {
+                    "action_arguments": {
+                        "newname": "#{inputVCF | basename}.filteredVCF"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputVCF"
+                }, 
+                "RenameDatasetActionoutput_html": {
+                    "action_arguments": {
+                        "newname": "#{inputVCF | basename}.VCFFiltering.graphs"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_html"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", 
+            "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\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }, 
+    "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a"
+}
\ No newline at end of file