changeset 20:1a45e744ca0f draft

Uploaded

--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,648 +0,0 @@
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--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.32.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-            "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

--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,424 +0,0 @@
-{
-    "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": [
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-                    "name": "output_file", 
-                    "type": "sam"
-                }
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-            "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": []
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-        "6": {
-            "annotation": "", 
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-            "input_connections": {
-                "input_file": {
-                    "id": 4, 
-                    "output_name": "output_fasta"
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-                    "type": "data"
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-                "top": 331
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-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
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-                "source|ref_file": {
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-            "inputs": [], 
-            "name": "SAM-to-BAM", 
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-                    "type": "bam"
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-            ], 
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-                "left": 1113, 
-                "top": 200
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-            "post_job_actions": {}, 
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-            "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": []
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-        "8": {
-            "annotation": "", 
-            "id": 8, 
-            "input_connections": {
-                "reference_source|input_bams_0|input_bam": {
-                    "id": 7, 
-                    "output_name": "output1"
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-                "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", 
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-            "type": "tool", 
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-            "input_connections": {
-                "input_file": {
-                    "id": 8, 
-                    "output_name": "output_mpileup"
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-            "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

--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-{
-    "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
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\ No newline at end of file

--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,260 +0,0 @@
-{
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-    "annotation": "", 
-    "format-version": "0.1", 
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-            "tool_errors": null, 
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-            "tool_state": "{\"name\": \"READ1\"}", 
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-            "inputs": [
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-            "type": "data_input", 
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-                    "output_name": "output"
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-                    "type": "fastqsanger"
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\ No newline at end of file

--- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.42.ga	Wed Aug 20 12:32:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,831 +0,0 @@
-{
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-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "Rapsodyn v1.42", 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/repository_dependencies.xml	Wed Aug 20 12:36:00 2014 -0400
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
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