annotate Galaxy-Workflow-MMuFF.ga @ 6:2aa99b7f90f4 draft default tip

Deleted selected files

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    "a_galaxy_workflow": "true", 
    "annotation": "", 
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            "input_connections": {}, 
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                {
                    "description": "Human RNA-seq paired reads left mates", 
                    "name": "Forward reads fastq"
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                "top": 314
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            "tool_id": null, 
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            "tool_version": null, 
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            "annotation": "Human RNA-seq paired reads right mates", 
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                {
                    "description": "Human RNA-seq paired reads right mates", 
                    "name": "Reverse reads fastq"
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            "name": "Input dataset", 
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                "left": 249, 
                "top": 410
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                {
                    "description": "Known SNPs  - dbSNP.vcf", 
                    "name": "VCF file of known variants (dbSNP)"
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                "top": 576
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            "type": "data_input", 
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                    "output_name": "output"
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            "inputs": [
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                    "name": "input_type"
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            "name": "FASTQ Groomer", 
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                    "name": "output_file", 
                    "type": "fastqsanger"
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            "annotation": "Convert quality scores to sanger scale", 
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                    "id": 1, 
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                    "description": "runtime parameter for tool FASTQ Groomer", 
                    "name": "input_type"
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            "name": "FASTQ Groomer", 
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                    "name": "output_file", 
                    "type": "fastqsanger"
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                    "description": "runtime parameter for tool Tophat for Illumina", 
                    "name": "singlePaired"
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                    "name": "insertions", 
                    "type": "bed"
                }, 
                {
                    "name": "deletions", 
                    "type": "bed"
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                {
                    "name": "junctions", 
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            "name": "Filter SAM or BAM", 
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                    "name": "output1", 
                    "type": "sam"
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                "left": 1154, 
                "top": 366
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            "name": "flagstat", 
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                    "type": "txt"
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            "annotation": "Remove duplicate reads", 
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                    "type": "html"
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                    "name": "output_interval", 
                    "type": "gatk_interval"
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                    "type": "bam"
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                    "type": "html"
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