Mercurial > repos > jjohnson > mmuff
changeset 6:2aa99b7f90f4 draft default tip
Deleted selected files
| author | jjohnson |
|---|---|
| date | Thu, 30 May 2013 11:27:21 -0400 |
| parents | 60a6f2d92058 |
| children | |
| files | Galaxy-Workflow-MMuFF_v1.2.ga |
| diffstat | 1 files changed, 0 insertions(+), 927 deletions(-) [+] |
line wrap: on
line diff
--- a/Galaxy-Workflow-MMuFF_v1.2.ga Sun May 26 08:17:53 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,927 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "MMuFF_Human_v1.2", - "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": 2327, - "top": 785 - }, - "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": [], - "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\\\": \\\"20\\\", \\\"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\\\": \\\"80\\\"}\"}", - "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": "2.2", - "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": 4421, - "top": 312 - }, - "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/3.1", - "tool_state": "{\"input\": \"null\", \"dbSnp\": \"null\", \"__page__\": 0}", - "tool_version": "3.1", - "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": 4724, - "top": 460 - }, - "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/3.1", - "tool_state": "{\"input\": \"null\", \"dbSnp\": \"null\", \"__page__\": 0}", - "tool_version": "3.1", - "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": 5043, - "top": 510 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", - "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"input\": \"null\"}", - "tool_version": "3.1", - "type": "tool", - "user_outputs": [] - }, - "21": { - "annotation": "Use Genome from Ensembl, e.g GRCh37.68 so we get ensembl transcript name info", - "id": 21, - "input_connections": { - "input": { - "id": 20, - "output_name": "output" - } - }, - "inputs": [], - "name": "SnpEff", - "outputs": [ - { - "name": "output", - "type": "tabular" - }, - { - "name": "statsFile", - "type": "html" - } - ], - "position": { - "left": 5277, - "top": 469 - }, - "post_job_actions": { - "HideDatasetActionstatsFile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "statsFile" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.1", - "tool_state": "{\"filterHomHet\": \"\\\"\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"filterOut\": \"[\\\"downstream\\\", \\\"intergenic\\\", \\\"intron\\\", \\\"upstream\\\", \\\"utr\\\"]\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"\\\"\", \"__page__\": 0, \"udLength\": \"\\\"0\\\"\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"offset\": \"\\\"\\\"\", \"input\": \"null\"}", - "tool_version": "3.1", - "type": "tool", - "user_outputs": [] - }, - "22": { - "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", - "id": 22, - "input_connections": { - "input": { - "id": 21, - "output_name": "output" - } - }, - "inputs": [], - "name": "SnpSift Filter", - "outputs": [ - { - "name": "output", - "type": "vcf" - } - ], - "position": { - "left": 5595, - "top": 432 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", - "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"input\": \"null\"}", - "tool_version": "3.1", - "type": "tool", - "user_outputs": [] - }, - "23": { - "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING \nvariants", - "id": 23, - "input_connections": { - "input": { - "id": 21, - "output_name": "output" - } - }, - "inputs": [], - "name": "SnpSift Filter", - "outputs": [ - { - "name": "output", - "type": "vcf" - } - ], - "position": { - "left": 5600, - "top": 611 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", - "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"input\": \"null\"}", - "tool_version": "3.1", - "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": 5828, - "top": 407 - }, - "post_job_actions": { - "HideDatasetActionhtml_report": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "html_report" - }, - "HideDatasetActiontext_report": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "text_report" - }, - "HideDatasetActiontsv_report": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "tsv_report" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", - "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", - "tool_version": "1.1", - "type": "tool", - "user_outputs": [] - }, - "25": { - "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", - "id": 25, - "input_connections": { - "snp_effect_vcf": { - "id": 23, - "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": 5832, - "top": 566 - }, - "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/1.0", - "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", - "tool_version": "1.1", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file