annotate Galaxy-Workflow-MMuFLR_Human_from_MPileup_v1.4.ga @ 1:53a99a00d5ec

Deleted selected files

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    "annotation": "", 
    "format-version": "0.1", 
    "name": "MMuFLR_Human_from_MPileup_v1.4", 
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            "annotation": "Tabular output from SAMtools mpileup", 
            "id": 0, 
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                {
                    "description": "Tabular output from SAMtools mpileup", 
                    "name": "Output from SAMtools MPileup"
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            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 273
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            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Output from SAMtools MPileup\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "Known SNPs  - dbSNP.vcf", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Known SNPs  - dbSNP.vcf", 
                    "name": "VCF file of known variants (dbSNP)"
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            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 432, 
                "top": 403
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            "tool_id": null, 
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            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
                    "name": "VCF file of additional known variants "
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            "name": "Input dataset", 
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            "position": {
                "left": 818, 
                "top": 453
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            "tool_id": null, 
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            "tool_version": null, 
            "type": "data_input", 
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            "id": 3, 
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                    "id": 0, 
                    "output_name": "output"
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            "inputs": [
                {
                    "description": "runtime parameter for tool Pileup to VCF", 
                    "name": "min_base_qual"
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            "name": "Pileup to VCF", 
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                {
                    "name": "output_file", 
                    "type": "vcf"
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            ], 
            "position": {
                "left": 459, 
                "top": 200
            }, 
            "post_job_actions": {}, 
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            "tool_version": "2.0", 
            "type": "tool", 
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        "4": {
            "annotation": "Annotate the ID field with dbSNP IDs.", 
            "id": 4, 
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                    "id": 1, 
                    "output_name": "output"
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                "input": {
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            "inputs": [], 
            "name": "SnpSift Annotate", 
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                    "name": "output", 
                    "type": "vcf"
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                "top": 256
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            "type": "tool", 
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            "annotation": "Annotate the ID field with users known variant IDs.", 
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                    "output_name": "output"
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                "input": {
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            "inputs": [], 
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                    "type": "vcf"
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            "type": "tool", 
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            "annotation": "Filter out chrM variations and any variant with an annotated ID", 
            "id": 6, 
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                    "id": 5, 
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                    "type": "vcf"
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            "inputs": [], 
            "name": "SnpEff", 
            "outputs": [
                {
                    "name": "snpeff_output", 
                    "type": "vcf"
                }, 
                {
                    "name": "statsFile", 
                    "type": "html"
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            ], 
            "position": {
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            "tool_version": "3.2", 
            "type": "tool", 
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        "8": {
            "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "snpeff_output"
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            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
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                    "name": "output", 
                    "type": "vcf"
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            ], 
            "position": {
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                "top": 310
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            "post_job_actions": {}, 
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            "tool_version": "3.2", 
            "type": "tool", 
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        "9": {
            "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants", 
            "id": 9, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "snpeff_output"
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            "inputs": [], 
            "name": "SnpSift Filter", 
            "outputs": [
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                    "name": "output", 
                    "type": "vcf"
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            "position": {
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            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
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            "inputs": [], 
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            "outputs": [
                {
                    "name": "html_report", 
                    "type": "html"
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                {
                    "name": "tsv_report", 
                    "type": "tabular"
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                {
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        "11": {
            "annotation": "Ignore variations in SPLICE donor/acceptor regions", 
            "id": 11, 
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                    "id": 9, 
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                    "type": "vcf"
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            "type": "tool", 
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            "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", 
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                    "id": 11, 
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            "inputs": [], 
            "name": "SnpEff Ensembl CDS", 
            "outputs": [
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                    "type": "html"
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