changeset 21:67ac3c7bcdeb draft

Uploaded
author mcharles
date Wed, 20 Aug 2014 12:37:55 -0400
parents 1a45e744ca0f
children afaf2e8aedcc
files rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.32.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.42.ga rapsodyn/repository_dependencies.xml
diffstat 7 files changed, 2909 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,648 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.31", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ1"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ2"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ASSEMBLY"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 370
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "DUBIOUS POSITION"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 455
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 331
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input_fasta": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "fastaGroomerForMakeBlastdb", 
+            "outputs": [
+                {
+                    "name": "output_fasta", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 462
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastaGroomerForMakeBlastdb", 
+            "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_combo", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_combo_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 756, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/nikhil-joshi/sickle/sickle/1.33", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe_sep\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 2}\", \"trunc_n\": \"\\\"False\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.33", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input_file": {
+                    "id": 6, 
+                    "output_name": "output_fasta"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ makeblastdb", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "data"
+                }
+            ], 
+            "position": {
+                "left": 756, 
+                "top": 528
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
+            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 7, 
+                    "output_name": "output_paired1"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 7, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_combo", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_combo_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 1084, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/nikhil-joshi/sickle/sickle/1.33", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe_sep\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 2}\", \"trunc_n\": \"\\\"True\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.33", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "genomeSource|ownFile": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "paired|input1": {
+                    "id": 9, 
+                    "output_name": "output_paired1"
+                }, 
+                "paired|input2": {
+                    "id": 9, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1412, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
+            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input_sam_file": {
+                    "id": 10, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersamunique", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1676, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "filtersamunique", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input1": {
+                    "id": 11, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 2004, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "source|input1": {
+                    "id": 12, 
+                    "output_name": "output1"
+                }, 
+                "source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 2332, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 13, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2560, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "input_file": {
+                    "id": 14, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2886, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input_listA": {
+                    "id": 15, 
+                    "output_name": "output_file"
+                }, 
+                "input_listB": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 3214, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3542, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 8, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 3870, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "input_blastxml_file": {
+                    "id": 18, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilteronblastxml", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4172, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilteronblastxml", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.32.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,632 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.32", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ1"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 404
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ2"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 489
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ASSEMBLY"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 574
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "DUBIOUS POSITION"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 659
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 535
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input_fasta": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "fastaGroomerForMakeBlastdb", 
+            "outputs": [
+                {
+                    "name": "output_fasta", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 666
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastaGroomerForMakeBlastdb", 
+            "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 762, 
+                "top": 245
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input_file": {
+                    "id": 6, 
+                    "output_name": "output_fasta"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ makeblastdb", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "data"
+                }
+            ], 
+            "position": {
+                "left": 756, 
+                "top": 732
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
+            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 7, 
+                    "output_name": "output_paired1"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 7, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "genomeSource|ownFile": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "paired|input1": {
+                    "id": 9, 
+                    "output_name": "output_paired1"
+                }, 
+                "paired|input2": {
+                    "id": 9, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1412, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
+            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input_sam_file": {
+                    "id": 10, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersamunique", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1676, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "filtersamunique", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input1": {
+                    "id": 11, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 2004, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "source|input1": {
+                    "id": 12, 
+                    "output_name": "output1"
+                }, 
+                "source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 2332, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 13, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2560, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "input_file": {
+                    "id": 14, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2886, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input_listA": {
+                    "id": 15, 
+                    "output_name": "output_file"
+                }, 
+                "input_listB": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 3214, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3542, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 8, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 3870, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "input_blastxml_file": {
+                    "id": 18, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilteronblastxml", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4172, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilteronblastxml", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,424 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.33 - Filtering", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "SAM"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 229, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"SAM\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ASSEMBLY"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 229, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "DUBIOUS POSITION"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 229, 
+                "top": 370
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input1": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 457, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_fasta": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "fastaGroomerForMakeBlastdb", 
+            "outputs": [
+                {
+                    "name": "output_fasta", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 457, 
+                "top": 358
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastaGroomerForMakeBlastdb", 
+            "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input_sam_file": {
+                    "id": 3, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersamunique", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 785, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "filtersamunique", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input_file": {
+                    "id": 4, 
+                    "output_name": "output_fasta"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ makeblastdb", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "data"
+                }
+            ], 
+            "position": {
+                "left": 785, 
+                "top": 331
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
+            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "source|input1": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }, 
+                "source|ref_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1113, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 7, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1341, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input_file": {
+                    "id": 8, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 1667, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "input_listA": {
+                    "id": 9, 
+                    "output_name": "output_file"
+                }, 
+                "input_listB": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 1995, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 10, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 2323, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 6, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 11, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 2651, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "input_blastxml_file": {
+                    "id": 12, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 10, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilteronblastxml", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2953, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilteronblastxml", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,114 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.33 - Mapping", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ASSEMBLY"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 245.64999389648438, 
+                "top": 273.816650390625
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ1 TRIMMED"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 243.64999389648438, 
+                "top": 358.816650390625
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ1 TRIMMED\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ2 TRIMMED"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 243.64999389648438, 
+                "top": 443.816650390625
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ2 TRIMMED\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "genomeSource|ownFile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "paired|input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "paired|input2": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 531.6500244140625, 
+                "top": 334.816650390625
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
+            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,260 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.33 - Preparation", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ1"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 424
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ2"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 509
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 424
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 555
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 2, 
+                    "output_name": "output_file"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 3, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 762, 
+                "top": 265
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "HideDatasetActionoutput_paired2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired2"
+                }, 
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 4, 
+                    "output_name": "output_paired1"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 4, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 1085, 
+                "top": 224
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }, 
+                "RenameDatasetActionoutput_paired1": {
+                    "action_arguments": {
+                        "newname": "read1_trimmed"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "RenameDatasetActionoutput_paired2": {
+                    "action_arguments": {
+                        "newname": "read2_trimmed"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.42.ga	Wed Aug 20 12:37:55 2014 -0400
@@ -0,0 +1,831 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Rapsodyn v1.42", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ1"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 199.99998474121094, 
+                "top": 404
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "READ2"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 199.99998474121094, 
+                "top": 489
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"READ2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ASSEMBLY"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 199.99998474121094, 
+                "top": 574
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "DUBIOUS POSITION"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 203.99998474121094, 
+                "top": 663.0000305175781
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 427.99998474121094, 
+                "top": 404
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 427.99998474121094, 
+                "top": 535
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 5, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 762, 
+                "top": 245
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "HideDatasetActionoutput_paired2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired2"
+                }, 
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 6, 
+                    "output_name": "output_paired1"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 6, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "HideDatasetActionoutput_paired2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired2"
+                }, 
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "genomeSource|ownFile": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "paired|input1": {
+                    "id": 7, 
+                    "output_name": "output_paired1"
+                }, 
+                "paired|input2": {
+                    "id": 7, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1412, 
+                "top": 404
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
+            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input_sam_file": {
+                    "id": 8, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersam_mapped_and_unique", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1773, 
+                "top": 339.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "filtersam_mapped_and_unique", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "source|input1": {
+                    "id": 9, 
+                    "output_name": "output_file"
+                }, 
+                "source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 2332, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 10, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2559.9998779296875, 
+                "top": 404
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_log": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
+                }, 
+                "HideDatasetActionoutput_mpileup": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input_file": {
+                    "id": 11, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2885.9998779296875, 
+                "top": 404
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "input_listA": {
+                    "id": 12, 
+                    "output_name": "output_file"
+                }, 
+                "input_listB": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 3213.9998779296875, 
+                "top": 404
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "input1": {
+                    "id": 13, 
+                    "output_name": "output_file"
+                }, 
+                "input2": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "tempo2", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "output2", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 3491.9998779296875, 
+                "top": 622.5000305175781
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
+                }, 
+                "HideDatasetActionoutput2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output2"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "tempo2", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"out1_format\": \"\\\"pileup\\\"\", \"out2_format\": \"\\\"fasta\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 14, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3792.9998779296875, 
+                "top": 510
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input_fasta": {
+                    "id": 14, 
+                    "output_name": "output2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "fastaGroomerForMakeBlastdb", 
+            "outputs": [
+                {
+                    "name": "output_fasta", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3740.9998779296875, 
+                "top": 910.0000305175781
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_fasta": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_fasta"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "fastaGroomerForMakeBlastdb", 
+            "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_file": {
+                    "id": 16, 
+                    "output_name": "output_fasta"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ makeblastdb", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "data"
+                }
+            ], 
+            "position": {
+                "left": 4046.9998779296875, 
+                "top": 935.0000305175781
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutfile": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outfile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
+            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 17, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 15, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 4276.9998779296875, 
+                "top": 702.0000305175781
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "input_blastxml_file": {
+                    "id": 18, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 14, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilteronblastxml", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4533.9998779296875, 
+                "top": 479
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilteronblastxml", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "20": {
+            "annotation": "", 
+            "id": 20, 
+            "input_connections": {
+                "input_blast_filtered_file": {
+                    "id": 19, 
+                    "output_name": "output_file"
+                }, 
+                "input_list_filtered_file": {
+                    "id": 13, 
+                    "output_name": "output_file"
+                }, 
+                "input_mpileup_filtered_file": {
+                    "id": 12, 
+                    "output_name": "output_file"
+                }, 
+                "input_mpileup_row_file": {
+                    "id": 11, 
+                    "output_name": "output_mpileup"
+                }, 
+                "input_read1_row_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "input_read1_trimmed_file": {
+                    "id": 6, 
+                    "output_name": "output_paired1"
+                }, 
+                "input_read1_trimmednoN_file": {
+                    "id": 7, 
+                    "output_name": "output_paired1"
+                }, 
+                "input_read2_row_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input_read2_trimmed_file": {
+                    "id": 6, 
+                    "output_name": "output_paired2"
+                }, 
+                "input_read2_trimmednoN_file": {
+                    "id": 7, 
+                    "output_name": "output_paired2"
+                }, 
+                "input_sam_filtered_file": {
+                    "id": 9, 
+                    "output_name": "output_file"
+                }, 
+                "input_sam_row_file": {
+                    "id": 8, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "rapsodyn_stats", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 4964.0001220703125, 
+                "top": 427.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "rapsodyn_stats", 
+            "tool_state": "{\"input_read1_trimmed_file\": \"null\", \"input_read2_trimmednoN_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_read2_trimmed_file\": \"null\", \"__page__\": 0, \"input_sam_row_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_mpileup_filtered_file\": \"null\", \"input_read1_trimmednoN_file\": \"null\", \"input_assembly_file\": \"null\", \"input_sam_filtered_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_mpileup_row_file\": \"null\", \"input_list_filtered_file\": \"null\", \"input_blast_filtered_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- a/rapsodyn/repository_dependencies.xml	Wed Aug 20 12:36:00 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Rapsodyn worflow needed repository">
-     <repository changeset_revision="c70137414dcd" name="sickle" owner="nikhil-joshi" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="1298445c852b" name="fastq_groomer" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="b4427dbb6ced" name="bwa_wrappers" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="9710e9bcc5f3" name="samtools_filter" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" />
-     <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-</repositories>