Mercurial > repos > jjohnson > mmuflr
changeset 0:4f70b23c497a
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 04 Jun 2013 09:51:17 -0400 |
| parents | |
| children | 53a99a00d5ec |
| files | ._Galaxy-Workflow-MMuFLR_Human_from_MPileup_v1.4.ga ._Galaxy-Workflow-MMuFLR_Human_germline_v1.4.ga ._Galaxy-Workflow-MMuFLR_Human_v1.4.ga Galaxy-Workflow-MMuFLR_Human_from_MPileup_v1.4.ga Galaxy-Workflow-MMuFLR_Human_germline_v1.4.ga Galaxy-Workflow-MMuFLR_Human_v1.4.ga |
| diffstat | 6 files changed, 1978 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MMuFLR_Human_from_MPileup_v1.4.ga Tue Jun 04 09:51:17 2013 -0400 @@ -0,0 +1,424 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MMuFLR_Human_from_MPileup_v1.4", + "steps": { + "0": { + "annotation": "Tabular output from SAMtools mpileup", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Tabular output from SAMtools mpileup", + "name": "Output from SAMtools MPileup" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 273 + }, + "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)" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 432, + "top": 403 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", + "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 " + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 818, + "top": 453 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF file of additional known variants \"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nLeave VCF_ID blank for tumor sample", + "id": 3, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Pileup to VCF", + "name": "min_base_qual" + } + ], + "name": "Pileup to VCF", + "outputs": [ + { + "name": "output_file", + "type": "vcf" + } + ], + "position": { + "left": 459, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", + "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", + "tool_version": "2.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "Annotate the ID field with dbSNP IDs.", + "id": 4, + "input_connections": { + "dbSnp": { + "id": 1, + "output_name": "output" + }, + "input": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "SnpSift Annotate", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 751, + "top": 256 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", + "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "Annotate the ID field with users known variant IDs.", + "id": 5, + "input_connections": { + "dbSnp": { + "id": 2, + "output_name": "output" + }, + "input": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Annotate", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 1134, + "top": 284 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", + "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "Filter out chrM variations and any variant with an annotated ID", + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 1488, + "top": 378 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff", + "outputs": [ + { + "name": "snpeff_output", + "type": "vcf" + }, + { + "name": "statsFile", + "type": "html" + } + ], + "position": { + "left": 1728, + "top": 310 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.2", + "tool_state": "{\"spliceSiteSize\": \"\\\"2\\\"\", \"filterHomHet\": \"\\\"no_filter\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"udLength\": \"\\\"0\\\"\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"no_filter\\\"\", \"__page__\": 0, \"filterOut\": \"[\\\"no-downstream\\\", \\\"no-intergenic\\\", \\\"no-intron\\\", \\\"no-upstream\\\", \\\"no-utr\\\"]\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"regulation\": \"null\", \"generate_stats\": \"\\\"True\\\"\", \"noLog\": \"\\\"True\\\"\", \"chr\": \"\\\"\\\"\", \"intervals\": \"null\", \"offset\": \"\\\"\\\"\", \"input\": \"null\", \"transcripts\": \"null\", \"annotations\": \"[\\\"hgvs\\\", \\\"lof\\\"]\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", + "id": 8, + "input_connections": { + "input": { + "id": 7, + "output_name": "snpeff_output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 2061, + "top": 310 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants", + "id": 9, + "input_connections": { + "input": { + "id": 7, + "output_name": "snpeff_output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 2058, + "top": 475 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", + "id": 10, + "input_connections": { + "snp_effect_vcf": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff Ensembl CDS", + "outputs": [ + { + "name": "html_report", + "type": "html" + }, + { + "name": "tsv_report", + "type": "tabular" + }, + { + "name": "text_report", + "type": "text" + } + ], + "position": { + "left": 2491, + "top": 226 + }, + "post_job_actions": { + "HideDatasetActiontext_report": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_report" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", + "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", + "tool_version": "1.2", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "Ignore variations in SPLICE donor/acceptor regions", + "id": 11, + "input_connections": { + "input": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 2281, + "top": 409 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"True\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[ANY].EFFECT =~ 'SPLICE' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", + "id": 12, + "input_connections": { + "snp_effect_vcf": { + "id": 11, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff Ensembl CDS", + "outputs": [ + { + "name": "html_report", + "type": "html" + }, + { + "name": "tsv_report", + "type": "tabular" + }, + { + "name": "text_report", + "type": "text" + } + ], + "position": { + "left": 2497, + "top": 381 + }, + "post_job_actions": { + "HideDatasetActiontext_report": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_report" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", + "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", + "tool_version": "1.2", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MMuFLR_Human_germline_v1.4.ga Tue Jun 04 09:51:17 2013 -0400 @@ -0,0 +1,609 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MMuFLR_Human_germline_v1.4", + "steps": { + "0": { + "annotation": "Human RNA-seq paired reads left mates", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Human RNA-seq paired reads left mates", + "name": "Forward reads fastq" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 240, + "top": 287 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Forward reads fastq\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "Human RNA-seq paired reads right mates", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Human RNA-seq paired reads right mates", + "name": "Reverse reads fastq" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 249, + "top": 383 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reverse reads fastq\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "Known SNPs - dbSNP.vcf", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Known SNPs - dbSNP.vcf", + "name": "VCF file of known variants (dbSNP)" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 2327, + "top": 758 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "Convert quality scores to sanger scale", + "id": 3, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Groomer", + "name": "input_type" + } + ], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 510, + "top": 264 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastq_groomer", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "Convert quality scores to sanger scale", + "id": 4, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Groomer", + "name": "input_type" + } + ], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 505, + "top": 404 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastq_groomer", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "Map paired reads to reference genome", + "id": 5, + "input_connections": { + "input1": { + "id": 3, + "output_name": "output_file" + }, + "singlePaired|input2": { + "id": 4, + "output_name": "output_file" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Tophat for Illumina", + "name": "singlePaired" + } + ], + "name": "Tophat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 884, + "top": 305 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + }, + "HideDatasetActionjunctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "junctions" + } + }, + "tool_errors": null, + "tool_id": "tophat", + "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", + "tool_version": "1.5.0", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)", + "id": 6, + "input_connections": { + "input1": { + "id": 5, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "name": "Filter SAM or BAM", + "outputs": [ + { + "name": "output1", + "type": "sam" + } + ], + "position": { + "left": 1154, + "top": 339 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "samtools_filter", + "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "input1": { + "id": 6, + "output_name": "output1" + } + }, + "inputs": [], + "name": "flagstat", + "outputs": [ + { + "name": "output1", + "type": "txt" + } + ], + "position": { + "left": 1505, + "top": 296 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "samtools_flagstat", + "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "Add Read Group info required by GATK tools", + "id": 8, + "input_connections": { + "inputFile": { + "id": 6, + "output_name": "output1" + } + }, + "inputs": [], + "name": "Add or Replace Groups", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1506, + "top": 476 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", + "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "Synchronize paired reads", + "id": 9, + "input_connections": { + "input_file": { + "id": 8, + "output_name": "outFile" + } + }, + "inputs": [], + "name": "Paired Read Mate Fixer", + "outputs": [ + { + "name": "out_file", + "type": "bam" + } + ], + "position": { + "left": 1841, + "top": 348 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", + "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "Remove duplicate reads", + "id": 10, + "input_connections": { + "input_file": { + "id": 9, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "Mark Duplicate reads", + "outputs": [ + { + "name": "out_file", + "type": "bam" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 2086, + "top": 333 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", + "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "Reorder BAM for GATK tools", + "id": 11, + "input_connections": { + "inputFile": { + "id": 10, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "Reorder SAM/BAM", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 2401, + "top": 305 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", + "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "reference_source|input_bam": { + "id": 11, + "output_name": "outFile" + }, + "rod_bind_0|rod_bind_type|input_rod": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "Realigner Target Creator", + "outputs": [ + { + "name": "output_interval", + "type": "gatk_interval" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 2565, + "top": 491 + }, + "post_job_actions": { + "HideDatasetActionoutput_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_log" + } + }, + "tool_errors": null, + "tool_id": "gatk_realigner_target_creator", + "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", + "tool_version": "0.0.4", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "Perform local realignments for indels", + "id": 13, + "input_connections": { + "reference_source|input_bam": { + "id": 11, + "output_name": "outFile" + }, + "target_intervals": { + "id": 12, + "output_name": "output_interval" + } + }, + "inputs": [], + "name": "Indel Realigner", + "outputs": [ + { + "name": "output_bam", + "type": "bam" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 2811, + "top": 324 + }, + "post_job_actions": { + "HideDatasetActionoutput_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_log" + } + }, + "tool_errors": null, + "tool_id": "gatk_indel_realigner", + "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", + "tool_version": "0.0.6", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "Check again for duplicate reads and eliminate", + "id": 14, + "input_connections": { + "input_file": { + "id": 13, + "output_name": "output_bam" + } + }, + "inputs": [], + "name": "Mark Duplicate reads", + "outputs": [ + { + "name": "out_file", + "type": "bam" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 3174, + "top": 291 + }, + "post_job_actions": { + "HideDatasetActionhtml_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "html_file" + }, + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", + "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "Determine base calls at each position", + "id": 15, + "input_connections": { + "reference_source|input_bams_0|input_bam": { + "id": 14, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "MPileup", + "outputs": [ + { + "name": "output_mpileup", + "type": "pileup" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 3554, + "top": 265 + }, + "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": "samtools_mpileup", + "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nVCF_ID = germline", + "id": 16, + "input_connections": { + "input_file": { + "id": 15, + "output_name": "output_mpileup" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Pileup to VCF", + "name": "min_base_qual" + } + ], + "name": "Pileup to VCF", + "outputs": [ + { + "name": "output_file", + "type": "vcf" + } + ], + "position": { + "left": 3937, + "top": 258 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", + "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"germline\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", + "tool_version": "2.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MMuFLR_Human_v1.4.ga Tue Jun 04 09:51:17 2013 -0400 @@ -0,0 +1,945 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MMuFLR_Human_v1.4", + "steps": { + "0": { + "annotation": "Human RNA-seq paired reads left mates", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Human RNA-seq paired reads left mates", + "name": "Forward reads fastq" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 240, + "top": 314 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Forward reads fastq\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "Human RNA-seq paired reads right mates", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Human RNA-seq paired reads right mates", + "name": "Reverse reads fastq" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 249, + "top": 410 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reverse reads fastq\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "Known SNPs - dbSNP.vcf", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Known SNPs - dbSNP.vcf", + "name": "VCF file of known variants (dbSNP)" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 2362, + "top": 745 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "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": 3, + "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 " + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 4388, + "top": 576 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF file of additional known variants \"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "4": { + "annotation": "Convert quality scores to sanger scale", + "id": 4, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Groomer", + "name": "input_type" + } + ], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 510, + "top": 291 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastq_groomer", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "Convert quality scores to sanger scale", + "id": 5, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Groomer", + "name": "input_type" + } + ], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 505, + "top": 431 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastq_groomer", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "Map paired reads to reference genome", + "id": 6, + "input_connections": { + "input1": { + "id": 4, + "output_name": "output_file" + }, + "singlePaired|input2": { + "id": 5, + "output_name": "output_file" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Tophat for Illumina", + "name": "singlePaired" + } + ], + "name": "Tophat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 884, + "top": 332 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + }, + "HideDatasetActionjunctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "junctions" + } + }, + "tool_errors": null, + "tool_id": "tophat", + "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", + "tool_version": "1.5.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)", + "id": 7, + "input_connections": { + "input1": { + "id": 6, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "name": "Filter SAM or BAM", + "outputs": [ + { + "name": "output1", + "type": "sam" + } + ], + "position": { + "left": 1154, + "top": 366 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "samtools_filter", + "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input1": { + "id": 7, + "output_name": "output1" + } + }, + "inputs": [], + "name": "flagstat", + "outputs": [ + { + "name": "output1", + "type": "txt" + } + ], + "position": { + "left": 1505, + "top": 323 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "samtools_flagstat", + "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "Add Read Group info required by GATK tools", + "id": 9, + "input_connections": { + "inputFile": { + "id": 7, + "output_name": "output1" + } + }, + "inputs": [], + "name": "Add or Replace Groups", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1506, + "top": 503 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", + "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "Synchronize paired reads", + "id": 10, + "input_connections": { + "input_file": { + "id": 9, + "output_name": "outFile" + } + }, + "inputs": [], + "name": "Paired Read Mate Fixer", + "outputs": [ + { + "name": "out_file", + "type": "bam" + } + ], + "position": { + "left": 1841, + "top": 375 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", + "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "Remove duplicate reads", + "id": 11, + "input_connections": { + "input_file": { + "id": 10, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "Mark Duplicate reads", + "outputs": [ + { + "name": "out_file", + "type": "bam" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 2086, + "top": 360 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", + "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "Reorder BAM for GATK tools", + "id": 12, + "input_connections": { + "inputFile": { + "id": 11, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "Reorder SAM/BAM", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 2401, + "top": 332 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", + "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "reference_source|input_bam": { + "id": 12, + "output_name": "outFile" + }, + "rod_bind_0|rod_bind_type|input_rod": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "Realigner Target Creator", + "outputs": [ + { + "name": "output_interval", + "type": "gatk_interval" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 2565, + "top": 518 + }, + "post_job_actions": { + "HideDatasetActionoutput_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_log" + } + }, + "tool_errors": null, + "tool_id": "gatk_realigner_target_creator", + "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", + "tool_version": "0.0.4", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "Perform local realignments for indels", + "id": 14, + "input_connections": { + "reference_source|input_bam": { + "id": 12, + "output_name": "outFile" + }, + "target_intervals": { + "id": 13, + "output_name": "output_interval" + } + }, + "inputs": [], + "name": "Indel Realigner", + "outputs": [ + { + "name": "output_bam", + "type": "bam" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 2811, + "top": 351 + }, + "post_job_actions": { + "HideDatasetActionoutput_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_log" + } + }, + "tool_errors": null, + "tool_id": "gatk_indel_realigner", + "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", + "tool_version": "0.0.6", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "Check again for duplicate reads and eliminate", + "id": 15, + "input_connections": { + "input_file": { + "id": 14, + "output_name": "output_bam" + } + }, + "inputs": [], + "name": "Mark Duplicate reads", + "outputs": [ + { + "name": "out_file", + "type": "bam" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 3174, + "top": 318 + }, + "post_job_actions": { + "HideDatasetActionhtml_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "html_file" + }, + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", + "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", + "tool_version": "1.56.0", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "Determine base calls at each position", + "id": 16, + "input_connections": { + "reference_source|input_bams_0|input_bam": { + "id": 15, + "output_name": "out_file" + } + }, + "inputs": [], + "name": "MPileup", + "outputs": [ + { + "name": "output_mpileup", + "type": "pileup" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 3554, + "top": 292 + }, + "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": "samtools_mpileup", + "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nLeave VCF_ID blank for tumor sample", + "id": 17, + "input_connections": { + "input_file": { + "id": 16, + "output_name": "output_mpileup" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Pileup to VCF", + "name": "min_base_qual" + } + ], + "name": "Pileup to VCF", + "outputs": [ + { + "name": "output_file", + "type": "vcf" + } + ], + "position": { + "left": 4029, + "top": 323 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", + "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", + "tool_version": "2.0", + "type": "tool", + "user_outputs": [] + }, + "18": { + "annotation": "Annotate the ID field with dbSNP IDs.", + "id": 18, + "input_connections": { + "dbSnp": { + "id": 2, + "output_name": "output" + }, + "input": { + "id": 17, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "SnpSift Annotate", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 4321, + "top": 379 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", + "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "19": { + "annotation": "Annotate the ID field with users known variant IDs.", + "id": 19, + "input_connections": { + "dbSnp": { + "id": 3, + "output_name": "output" + }, + "input": { + "id": 18, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Annotate", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 4704, + "top": 407 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2", + "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "20": { + "annotation": "Filter out chrM variations and any variant with an annotated ID", + "id": 20, + "input_connections": { + "input": { + "id": 19, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 5058, + "top": 501 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "21": { + "annotation": "", + "id": 21, + "input_connections": { + "input": { + "id": 20, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff", + "outputs": [ + { + "name": "snpeff_output", + "type": "vcf" + }, + { + "name": "statsFile", + "type": "html" + } + ], + "position": { + "left": 5298, + "top": 433 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.2", + "tool_state": "{\"spliceSiteSize\": \"\\\"2\\\"\", \"filterHomHet\": \"\\\"no_filter\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"udLength\": \"\\\"0\\\"\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"no_filter\\\"\", \"__page__\": 0, \"filterOut\": \"[\\\"no-downstream\\\", \\\"no-intergenic\\\", \\\"no-intron\\\", \\\"no-upstream\\\", \\\"no-utr\\\"]\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"regulation\": \"null\", \"generate_stats\": \"\\\"True\\\"\", \"noLog\": \"\\\"True\\\"\", \"chr\": \"\\\"\\\"\", \"intervals\": \"null\", \"offset\": \"\\\"\\\"\", \"input\": \"null\", \"transcripts\": \"null\", \"annotations\": \"[\\\"hgvs\\\", \\\"lof\\\"]\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "22": { + "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", + "id": 22, + "input_connections": { + "input": { + "id": 21, + "output_name": "snpeff_output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 5631, + "top": 433 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "23": { + "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants", + "id": 23, + "input_connections": { + "input": { + "id": 21, + "output_name": "snpeff_output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 5628, + "top": 598 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "24": { + "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", + "id": 24, + "input_connections": { + "snp_effect_vcf": { + "id": 22, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff Ensembl CDS", + "outputs": [ + { + "name": "html_report", + "type": "html" + }, + { + "name": "tsv_report", + "type": "tabular" + }, + { + "name": "text_report", + "type": "text" + } + ], + "position": { + "left": 6064, + "top": 345 + }, + "post_job_actions": { + "HideDatasetActiontext_report": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_report" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", + "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", + "tool_version": "1.2", + "type": "tool", + "user_outputs": [] + }, + "25": { + "annotation": "Ignore variations in SPLICE donor/acceptor regions", + "id": 25, + "input_connections": { + "input": { + "id": 23, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 5851, + "top": 532 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"True\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[ANY].EFFECT =~ 'SPLICE' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "3.2", + "type": "tool", + "user_outputs": [] + }, + "26": { + "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", + "id": 26, + "input_connections": { + "snp_effect_vcf": { + "id": 25, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff Ensembl CDS", + "outputs": [ + { + "name": "html_report", + "type": "html" + }, + { + "name": "tsv_report", + "type": "tabular" + }, + { + "name": "text_report", + "type": "text" + } + ], + "position": { + "left": 6067, + "top": 502 + }, + "post_job_actions": { + "HideDatasetActiontext_report": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_report" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", + "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", + "tool_version": "1.2", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file