# HG changeset patch # User urgi-team # Date 1448462057 18000 # Node ID 7557b71a92e702a4eeef9aa9075e5e8a3f5ece45 # Parent 33391dfcfc076993519314456713219d98275de6 Uploaded diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-creation_workflow_gandalf_2.0.ga --- a/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Wed Nov 18 10:54:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,384 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "workflow gandalf 1 set", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 288, - "top": 200 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 288, - "top": 285 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 288, - "top": 370 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "input_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "mdust", - "outputs": [ - { - "name": "output_masked_fasta", - "type": "fasta" - }, - { - "name": "output_tab", - "type": "tabular" - }, - { - "name": "output_bed", - "type": "bed" - } - ], - "position": { - "left": 571, - "top": 394 - }, - "post_job_actions": { - "RenameDatasetActionoutput_bed": { - "action_arguments": { - "newname": "#{input_file | basename}.bed" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_bed" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", - "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "fastq_input|fastq_input1": { - "id": 1, - "output_name": "output" - }, - "fastq_input|fastq_input2": { - "id": 2, - "output_name": "output" - }, - "reference_source|ref_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Map with BWA-MEM", - "outputs": [ - { - "name": "bam_output", - "type": "bam" - } - ], - "position": { - "left": 516, - "top": 200 - }, - "post_job_actions": { - "RenameDatasetActionbam_output": { - "action_arguments": { - "newname": "#{fastq_input1 | basename}.bam" - }, - "action_type": "RenameDatasetAction", - "output_name": "bam_output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.4.1", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "input1": { - "id": 4, - "output_name": "bam_output" - } - }, - "inputs": [], - "name": "mapQfilter", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 844, - "top": 200 - }, - "post_job_actions": { - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{input1 | basename}.filteredbam" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "", - "id": 6, - "input_connections": { - "inputFile": { - "id": 5, - "output_name": "output1" - } - }, - "inputs": [], - "name": "MarkDuplicates", - "outputs": [ - { - "name": "metrics_file", - "type": "txt" - }, - { - "name": "outFile", - "type": "bam" - } - ], - "position": { - "left": 1072, - "top": 200 - }, - "post_job_actions": { - "RenameDatasetActionoutFile": { - "action_arguments": { - "newname": "#{inputFile | basename}.markedBAM" - }, - "action_type": "RenameDatasetAction", - "output_name": "outFile" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", - "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", - "tool_version": "1.126.0", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "input1": { - "id": 6, - "output_name": "outFile" - } - }, - "inputs": [], - "name": "flagstat", - "outputs": [ - { - "name": "output1", - "type": "txt" - } - ], - "position": { - "left": 1400, - "top": 200 - }, - "post_job_actions": { - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{inupt1| basename}.stats" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "", - "id": 8, - "input_connections": { - "input_bams_0|input_bam": { - "id": 6, - "output_name": "outFile" - }, - "reference_source|ref_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Freebayes4Workflow", - "outputs": [ - { - "name": "output_vcf_default", - "type": "vcf" - }, - { - "name": "output_vcf_firstBAM", - "type": "vcf" - }, - { - "name": "output_vcf_rename", - "type": "vcf" - }, - { - "name": "output_failed_alleles_bed", - "type": "bed" - }, - { - "name": "output_trace", - "type": "txt" - } - ], - "position": { - "left": 1400, - "top": 313 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", - "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", - "tool_version": "0.5", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "", - "id": 9, - "input_connections": { - "BedFile_List|BedFiles_0|inputBed": { - "id": 3, - "output_name": "output_bed" - }, - "inputVCF": { - "id": 8, - "output_name": "output_vcf_firstBAM" - } - }, - "inputs": [], - "name": "VCFFiltering", - "outputs": [ - { - "name": "outputVCF", - "type": "vcf" - }, - { - "name": "output_html", - "type": "html" - } - ], - "position": { - "left": 1904, - "top": 265 - }, - "post_job_actions": { - "RenameDatasetActionoutputVCF": { - "action_arguments": { - "newname": "#{inputVCF | basename}.filteredVCF" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCF" - }, - "RenameDatasetActionoutput_html": { - "action_arguments": { - "newname": "#{inputVCF | basename}.VCFFiltering.graphs" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_html" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", - "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - } - }, - "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a" -} diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_1.0.ga --- a/Galaxy-Workflow-workflow_gandalf_1.0.ga Wed Nov 18 10:54:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,320 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "workflow gandalf 1.0", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 467, - "top": 200 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 467, - "top": 320 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 467, - "top": 440 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "fastq_input|fastq_input1": { - "id": 1, - "output_name": "output" - }, - "fastq_input|fastq_input2": { - "id": 2, - "output_name": "output" - }, - "reference_source|ref_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Map with BWA-MEM", - "outputs": [ - { - "name": "bam_output", - "type": "bam" - } - ], - "position": { - "left": 661, - "top": 204 - }, - "post_job_actions": { - "RenameDatasetActionbam_output": { - "action_arguments": { - "newname": "#{fastq_input1 | basename}.bam" - }, - "action_type": "RenameDatasetAction", - "output_name": "bam_output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.4.1", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "input1": { - "id": 3, - "output_name": "bam_output" - } - }, - "inputs": [], - "name": "mapQfilter", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 944, - "top": 161 - }, - "post_job_actions": { - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{input1 | basename}.bam" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "10.0.0.125:9009/repos/urgiteam/mapqfilter/mapQfilter/1.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "inputFile": { - "id": 4, - "output_name": "output1" - } - }, - "inputs": [], - "name": "MarkDuplicates", - "outputs": [ - { - "name": "metrics_file", - "type": "txt" - }, - { - "name": "outFile", - "type": "bam" - } - ], - "position": { - "left": 1121, - "top": 208 - }, - "post_job_actions": { - "RenameDatasetActionoutFile": { - "action_arguments": { - "newname": "#{inputFile | basename}.markedBAM" - }, - "action_type": "RenameDatasetAction", - "output_name": "outFile" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", - "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", - "tool_version": "1.126.0", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "", - "id": 6, - "input_connections": { - "input_bams_0|input_bam": { - "id": 5, - "output_name": "outFile" - }, - "reference_source|ref_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "FreeBayesFix", - "outputs": [ - { - "name": "output_vcf_default", - "type": "vcf" - }, - { - "name": "output_vcf_firstBAM", - "type": "vcf" - }, - { - "name": "output_vcf_rename", - "type": "vcf" - }, - { - "name": "output_failed_alleles_bed", - "type": "bed" - }, - { - "name": "output_trace", - "type": "txt" - } - ], - "position": { - "left": 1347, - "top": 320 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "10.0.0.125:9009/repos/urgiteam/freebayes/freebayes-fix/0.4", - "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", - "tool_version": "0.4", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "input1": { - "id": 5, - "output_name": "outFile" - } - }, - "inputs": [], - "name": "flagstat", - "outputs": [ - { - "name": "output1", - "type": "txt" - } - ], - "position": { - "left": 1395, - "top": 208 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "samtools_flagstat", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "", - "id": 8, - "input_connections": { - "inputVCF": { - "id": 6, - "output_name": "output_vcf_firstBAM" - } - }, - "inputs": [], - "name": "VCFFiltering", - "outputs": [ - { - "name": "outputVCF", - "type": "vcf" - }, - { - "name": "output_html", - "type": "html" - } - ], - "position": { - "left": 1714, - "top": 180 - }, - "post_job_actions": { - "RenameDatasetActionoutputVCF": { - "action_arguments": { - "newname": "#{inputVCF | basename}.filteredVCF" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCF" - } - }, - "tool_errors": null, - "tool_id": "10.0.0.125:9009/repos/urgiteam/vcfgandalftools/VCFFiltering/0.01", - "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"is_BedFile\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - } - }, - "uuid": "1a7a40af-5624-4049-a1dd-fee31e8731ee" -} \ No newline at end of file diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_1_set.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-workflow_gandalf_1_set.ga Wed Nov 25 09:34:17 2015 -0500 @@ -0,0 +1,384 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "workflow gandalf 1 set", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 128, + "top": 198 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genome reads forward " + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 157, + "top": 295 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Genome reads forward \"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genome read Reverse" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 193, + "top": 394 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Genome read Reverse\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "mdust", + "outputs": [ + { + "name": "output_masked_fasta", + "type": "fasta" + }, + { + "name": "output_tab", + "type": "tabular" + }, + { + "name": "output_bed", + "type": "bed" + } + ], + "position": { + "left": 571, + "top": 395 + }, + "post_job_actions": { + "RenameDatasetActionoutput_bed": { + "action_arguments": { + "newname": "#{input_file | basename}.bed" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", + "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "fastq_input|fastq_input1": { + "id": 1, + "output_name": "output" + }, + "fastq_input|fastq_input2": { + "id": 2, + "output_name": "output" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Map with BWA-MEM", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 516, + "top": 201 + }, + "post_job_actions": { + "RenameDatasetActionbam_output": { + "action_arguments": { + "newname": "#{fastq_input1 | basename}.bam" + }, + "action_type": "RenameDatasetAction", + "output_name": "bam_output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.4.1", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input1": { + "id": 4, + "output_name": "bam_output" + } + }, + "inputs": [], + "name": "mapQfilter", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 844, + "top": 201 + }, + "post_job_actions": { + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{input1 | basename}.filteredbam" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}", + "tool_version": "1.0", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "inputFile": { + "id": 5, + "output_name": "output1" + } + }, + "inputs": [], + "name": "MarkDuplicates", + "outputs": [ + { + "name": "metrics_file", + "type": "txt" + }, + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1072, + "top": 201 + }, + "post_job_actions": { + "RenameDatasetActionoutFile": { + "action_arguments": { + "newname": "#{inputFile | basename}.markedBAM" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", + "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.126.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "input1": { + "id": 6, + "output_name": "outFile" + } + }, + "inputs": [], + "name": "flagstat", + "outputs": [ + { + "name": "output1", + "type": "txt" + } + ], + "position": { + "left": 1400, + "top": 201 + }, + "post_job_actions": { + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{inupt1| basename}.stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input_bams_0|input_bam": { + "id": 6, + "output_name": "outFile" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Freebayes4Workflow", + "outputs": [ + { + "name": "output_vcf_default", + "type": "vcf" + }, + { + "name": "output_vcf_firstBAM", + "type": "vcf" + }, + { + "name": "output_vcf_rename", + "type": "vcf" + }, + { + "name": "output_failed_alleles_bed", + "type": "bed" + }, + { + "name": "output_trace", + "type": "txt" + } + ], + "position": { + "left": 1400, + "top": 314 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", + "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.5", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "BedFile_List|BedFiles_0|inputBed": { + "id": 3, + "output_name": "output_bed" + }, + "inputVCF": { + "id": 8, + "output_name": "output_vcf_firstBAM" + } + }, + "inputs": [], + "name": "VCFFiltering", + "outputs": [ + { + "name": "outputVCF", + "type": "vcf" + }, + { + "name": "output_html", + "type": "html" + } + ], + "position": { + "left": 1904, + "top": 266 + }, + "post_job_actions": { + "RenameDatasetActionoutputVCF": { + "action_arguments": { + "newname": "#{inputVCF | basename}.filteredVCF" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputVCF" + }, + "RenameDatasetActionoutput_html": { + "action_arguments": { + "newname": "#{inputVCF | basename}.VCFFiltering.graphs" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_html" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", + "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + }, + "uuid": "58cfd654-45c2-443f-9c8c-b862c0b4ca06" +} \ No newline at end of file diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_2_sets.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-workflow_gandalf_2_sets.ga Wed Nov 25 09:34:17 2015 -0500 @@ -0,0 +1,933 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "workflow gandalf 2 sets", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 248, + "top": 874 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "genome 1 reads forward" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 280, + "top": 979 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"genome 1 reads forward\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "genome 1 reads reverse" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 288, + "top": 1048 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"genome 1 reads reverse\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "genome 2 reads forward" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 346, + "top": 1206 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"genome 2 reads forward\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "genome 2 reads reverse" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 344, + "top": 1277 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"genome 2 reads reverse\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "mdust", + "outputs": [ + { + "name": "output_masked_fasta", + "type": "fasta" + }, + { + "name": "output_tab", + "type": "tabular" + }, + { + "name": "output_bed", + "type": "bed" + } + ], + "position": { + "left": 1419, + "top": 230 + }, + "post_job_actions": { + "HideDatasetActionoutput_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_bed" + }, + "HideDatasetActionoutput_masked_fasta": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_masked_fasta" + }, + "HideDatasetActionoutput_tab": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_tab" + }, + "RenameDatasetActionoutput_bed": { + "action_arguments": { + "newname": "#{input_file | basename}.bed" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", + "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "fastq_input|fastq_input1": { + "id": 1, + "output_name": "output" + }, + "fastq_input|fastq_input2": { + "id": 2, + "output_name": "output" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Map with BWA-MEM", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 758, + "top": 929 + }, + "post_job_actions": { + "HideDatasetActionbam_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "bam_output" + }, + "RenameDatasetActionbam_output": { + "action_arguments": { + "newname": "#{fastq_input1 | basename}.bam" + }, + "action_type": "RenameDatasetAction", + "output_name": "bam_output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.4.1", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "fastq_input|fastq_input1": { + "id": 3, + "output_name": "output" + }, + "fastq_input|fastq_input2": { + "id": 4, + "output_name": "output" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Map with BWA-MEM", + "outputs": [ + { + "name": "bam_output", + "type": "bam" + } + ], + "position": { + "left": 758, + "top": 1114 + }, + "post_job_actions": { + "HideDatasetActionbam_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "bam_output" + }, + "RenameDatasetActionbam_output": { + "action_arguments": { + "newname": "#{fastq_input1 | basename}.bam" + }, + "action_type": "RenameDatasetAction", + "output_name": "bam_output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.4.1", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input1": { + "id": 6, + "output_name": "bam_output" + } + }, + "inputs": [], + "name": "mapQfilter", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1086, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{input1 | basename}.filteredbam" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", + "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "input1": { + "id": 7, + "output_name": "bam_output" + } + }, + "inputs": [], + "name": "mapQfilter", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1086, + "top": 706 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{input1 | basename}.filteredbam" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", + "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "inputFile": { + "id": 8, + "output_name": "output1" + } + }, + "inputs": [], + "name": "MarkDuplicates", + "outputs": [ + { + "name": "metrics_file", + "type": "txt" + }, + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1314, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionmetrics_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "metrics_file" + }, + "HideDatasetActionoutFile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outFile" + }, + "RenameDatasetActionoutFile": { + "action_arguments": { + "newname": "#{inputFile | basename}.markedBAM" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", + "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.126.0", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "inputFile": { + "id": 9, + "output_name": "output1" + } + }, + "inputs": [], + "name": "MarkDuplicates", + "outputs": [ + { + "name": "metrics_file", + "type": "txt" + }, + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 1314, + "top": 751 + }, + "post_job_actions": { + "HideDatasetActionmetrics_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "metrics_file" + }, + "HideDatasetActionoutFile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outFile" + }, + "RenameDatasetActionoutFile": { + "action_arguments": { + "newname": "#{inputFile | basename}.markedBAM" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", + "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.126.0", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "input_bams_0|input_bam": { + "id": 10, + "output_name": "outFile" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Freebayes4Workflow", + "outputs": [ + { + "name": "output_vcf_default", + "type": "vcf" + }, + { + "name": "output_vcf_firstBAM", + "type": "vcf" + }, + { + "name": "output_vcf_rename", + "type": "vcf" + }, + { + "name": "output_failed_alleles_bed", + "type": "bed" + }, + { + "name": "output_trace", + "type": "txt" + } + ], + "position": { + "left": 1642, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionoutput_failed_alleles_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_failed_alleles_bed" + }, + "HideDatasetActionoutput_trace": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_trace" + }, + "HideDatasetActionoutput_vcf_default": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_default" + }, + "HideDatasetActionoutput_vcf_firstBAM": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_firstBAM" + }, + "HideDatasetActionoutput_vcf_rename": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_rename" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", + "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.5", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "input1": { + "id": 10, + "output_name": "outFile" + } + }, + "inputs": [], + "name": "flagstat", + "outputs": [ + { + "name": "output1", + "type": "txt" + } + ], + "position": { + "left": 1642, + "top": 1125 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{inupt1| basename}.stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "input_bams_0|input_bam": { + "id": 11, + "output_name": "outFile" + }, + "reference_source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Freebayes4Workflow", + "outputs": [ + { + "name": "output_vcf_default", + "type": "vcf" + }, + { + "name": "output_vcf_firstBAM", + "type": "vcf" + }, + { + "name": "output_vcf_rename", + "type": "vcf" + }, + { + "name": "output_failed_alleles_bed", + "type": "bed" + }, + { + "name": "output_trace", + "type": "txt" + } + ], + "position": { + "left": 1776, + "top": 1195 + }, + "post_job_actions": { + "HideDatasetActionoutput_failed_alleles_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_failed_alleles_bed" + }, + "HideDatasetActionoutput_trace": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_trace" + }, + "HideDatasetActionoutput_vcf_default": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_default" + }, + "HideDatasetActionoutput_vcf_firstBAM": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_firstBAM" + }, + "HideDatasetActionoutput_vcf_rename": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_vcf_rename" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", + "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.5", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "input1": { + "id": 11, + "output_name": "outFile" + } + }, + "inputs": [], + "name": "flagstat", + "outputs": [ + { + "name": "output1", + "type": "txt" + } + ], + "position": { + "left": 1642, + "top": 1770 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + }, + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "#{inupt1| basename}.stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "BedFile_List|BedFiles_0|inputBed": { + "id": 5, + "output_name": "output_bed" + }, + "inputVCF": { + "id": 12, + "output_name": "output_vcf_firstBAM" + } + }, + "inputs": [], + "name": "VCFFiltering", + "outputs": [ + { + "name": "outputVCF", + "type": "vcf" + }, + { + "name": "output_html", + "type": "html" + } + ], + "position": { + "left": 1970, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionoutputVCF": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputVCF" + }, + "HideDatasetActionoutput_html": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_html" + }, + "RenameDatasetActionoutputVCF": { + "action_arguments": { + "newname": "#{inputVCF | basename}.filteredVCF" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputVCF" + }, + "RenameDatasetActionoutput_html": { + "action_arguments": { + "newname": "#{inputVCF | basename}.VCFFiltering.graphs" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_html" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", + "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "BedFile_List|BedFiles_0|inputBed": { + "id": 5, + "output_name": "output_bed" + }, + "inputVCF": { + "id": 14, + "output_name": "output_vcf_firstBAM" + } + }, + "inputs": [], + "name": "VCFFiltering", + "outputs": [ + { + "name": "outputVCF", + "type": "vcf" + }, + { + "name": "output_html", + "type": "html" + } + ], + "position": { + "left": 1970, + "top": 778 + }, + "post_job_actions": { + "HideDatasetActionoutputVCF": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputVCF" + }, + "HideDatasetActionoutput_html": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_html" + }, + "RenameDatasetActionoutputVCF": { + "action_arguments": { + "newname": "#{inputVCF | basename}.filteredVCF" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputVCF" + }, + "RenameDatasetActionoutput_html": { + "action_arguments": { + "newname": "#{inputVCF | basename}.VCFFiltering.graphs" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_html" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", + "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "18": { + "annotation": "", + "id": 18, + "input_connections": { + "VCFFile_0|inputStrainVCF": { + "id": 16, + "output_name": "outputVCF" + }, + "VCFFile_1|inputStrainVCF": { + "id": 17, + "output_name": "outputVCF" + }, + "inputFasta": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "VCFStorage", + "outputs": [ + { + "name": "outputVCFStorage", + "type": "tabular" + } + ], + "position": { + "left": 2298, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionoutputVCFStorage": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outputVCFStorage" + }, + "RenameDatasetActionoutputVCFStorage": { + "action_arguments": { + "newname": "#{inputFasta | basename}.matrix" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputVCFStorage" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", + "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"VCFFile\": \"[{\\\"strainName\\\": \\\"strain1\\\", \\\"__index__\\\": 0, \\\"inputStrainVCF\\\": null}, {\\\"strainName\\\": \\\"strain2\\\", \\\"__index__\\\": 1, \\\"inputStrainVCF\\\": null}]\", \"inputFasta\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "19": { + "annotation": "", + "id": 19, + "input_connections": { + "inputTabular": { + "id": 18, + "output_name": "outputVCFStorage" + } + }, + "inputs": [], + "name": "VCFCarto", + "outputs": [ + { + "name": "outputVCFCarto", + "type": "tabular" + }, + { + "name": "output_html", + "type": "html" + }, + { + "name": "output_bed", + "type": "bed" + } + ], + "position": { + "left": 2618, + "top": 593 + }, + "post_job_actions": { + "HideDatasetActionoutput_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_bed" + }, + "HideDatasetActionoutput_html": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_html" + }, + "RenameDatasetActionoutputVCFCarto": { + "action_arguments": { + "newname": "#{inputTabular | basename}.red" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputVCFCarto" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01", + "tool_state": "{\"__page__\": 0, \"parentA\": \"\\\"strain1\\\"\", \"__rerun_remap_job_id__\": null, \"outputType\": \"\\\"raw\\\"\", \"parentH\": \"\\\"strain2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputTabular\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + }, + "uuid": "f217cc60-5c89-442b-80ee-3d055e407367" +} \ No newline at end of file diff -r 33391dfcfc07 -r 7557b71a92e7 Galaxy-Workflow-workflow_gandalf_3.0.ga --- a/Galaxy-Workflow-workflow_gandalf_3.0.ga Wed Nov 18 10:54:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,933 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "workflow gandalf 2 sets", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 258, - "top": 593 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 258, - "top": 685 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 252, - "top": 773 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 241, - "top": 853 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 245, - "top": 938 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "fastq_input|fastq_input1": { - "id": 2, - "output_name": "output" - }, - "fastq_input|fastq_input2": { - "id": 0, - "output_name": "output" - }, - "reference_source|ref_file": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Map with BWA-MEM", - "outputs": [ - { - "name": "bam_output", - "type": "bam" - } - ], - "position": { - "left": 527, - "top": 929 - }, - "post_job_actions": { - "HideDatasetActionbam_output": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "bam_output" - }, - "RenameDatasetActionbam_output": { - "action_arguments": { - "newname": "#{fastq_input1 | basename}.bam" - }, - "action_type": "RenameDatasetAction", - "output_name": "bam_output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.4.1", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "", - "id": 6, - "input_connections": { - "input_file": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "mdust", - "outputs": [ - { - "name": "output_masked_fasta", - "type": "fasta" - }, - { - "name": "output_tab", - "type": "tabular" - }, - { - "name": "output_bed", - "type": "bed" - } - ], - "position": { - "left": 1188, - "top": 230 - }, - "post_job_actions": { - "HideDatasetActionoutput_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_bed" - }, - "HideDatasetActionoutput_masked_fasta": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_masked_fasta" - }, - "HideDatasetActionoutput_tab": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_tab" - }, - "RenameDatasetActionoutput_bed": { - "action_arguments": { - "newname": "#{input_file | basename}.bed" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_bed" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", - "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "fastq_input|fastq_input1": { - "id": 3, - "output_name": "output" - }, - "fastq_input|fastq_input2": { - "id": 1, - "output_name": "output" - }, - "reference_source|ref_file": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Map with BWA-MEM", - "outputs": [ - { - "name": "bam_output", - "type": "bam" - } - ], - "position": { - "left": 527, - "top": 1114 - }, - "post_job_actions": { - "HideDatasetActionbam_output": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "bam_output" - }, - "RenameDatasetActionbam_output": { - "action_arguments": { - "newname": "#{fastq_input1 | basename}.bam" - }, - "action_type": "RenameDatasetAction", - "output_name": "bam_output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.4.1", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "", - "id": 8, - "input_connections": { - "input1": { - "id": 5, - "output_name": "bam_output" - } - }, - "inputs": [], - "name": "mapQfilter", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 855, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output1" - }, - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{input1 | basename}.filteredbam" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "", - "id": 9, - "input_connections": { - "input1": { - "id": 7, - "output_name": "bam_output" - } - }, - "inputs": [], - "name": "mapQfilter", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 855, - "top": 706 - }, - "post_job_actions": { - "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output1" - }, - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{input1 | basename}.filteredbam" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0", - "type": "tool", - "user_outputs": [] - }, - "10": { - "annotation": "", - "id": 10, - "input_connections": { - "inputFile": { - "id": 8, - "output_name": "output1" - } - }, - "inputs": [], - "name": "MarkDuplicates", - "outputs": [ - { - "name": "metrics_file", - "type": "txt" - }, - { - "name": "outFile", - "type": "bam" - } - ], - "position": { - "left": 1083, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionmetrics_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "metrics_file" - }, - "HideDatasetActionoutFile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outFile" - }, - "RenameDatasetActionoutFile": { - "action_arguments": { - "newname": "#{inputFile | basename}.markedBAM" - }, - "action_type": "RenameDatasetAction", - "output_name": "outFile" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", - "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", - "tool_version": "1.126.0", - "type": "tool", - "user_outputs": [] - }, - "11": { - "annotation": "", - "id": 11, - "input_connections": { - "inputFile": { - "id": 9, - "output_name": "output1" - } - }, - "inputs": [], - "name": "MarkDuplicates", - "outputs": [ - { - "name": "metrics_file", - "type": "txt" - }, - { - "name": "outFile", - "type": "bam" - } - ], - "position": { - "left": 1083, - "top": 751 - }, - "post_job_actions": { - "HideDatasetActionmetrics_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "metrics_file" - }, - "HideDatasetActionoutFile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outFile" - }, - "RenameDatasetActionoutFile": { - "action_arguments": { - "newname": "#{inputFile | basename}.markedBAM" - }, - "action_type": "RenameDatasetAction", - "output_name": "outFile" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", - "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", - "tool_version": "1.126.0", - "type": "tool", - "user_outputs": [] - }, - "12": { - "annotation": "", - "id": 12, - "input_connections": { - "input_bams_0|input_bam": { - "id": 10, - "output_name": "outFile" - }, - "reference_source|ref_file": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Freebayes4Workflow", - "outputs": [ - { - "name": "output_vcf_default", - "type": "vcf" - }, - { - "name": "output_vcf_firstBAM", - "type": "vcf" - }, - { - "name": "output_vcf_rename", - "type": "vcf" - }, - { - "name": "output_failed_alleles_bed", - "type": "bed" - }, - { - "name": "output_trace", - "type": "txt" - } - ], - "position": { - "left": 1411, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionoutput_failed_alleles_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_failed_alleles_bed" - }, - "HideDatasetActionoutput_trace": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_trace" - }, - "HideDatasetActionoutput_vcf_default": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_default" - }, - "HideDatasetActionoutput_vcf_firstBAM": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_firstBAM" - }, - "HideDatasetActionoutput_vcf_rename": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_rename" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", - "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", - "tool_version": "0.5", - "type": "tool", - "user_outputs": [] - }, - "13": { - "annotation": "", - "id": 13, - "input_connections": { - "input1": { - "id": 10, - "output_name": "outFile" - } - }, - "inputs": [], - "name": "flagstat", - "outputs": [ - { - "name": "output1", - "type": "txt" - } - ], - "position": { - "left": 1411, - "top": 1125 - }, - "post_job_actions": { - "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output1" - }, - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{inupt1| basename}.stats" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "14": { - "annotation": "", - "id": 14, - "input_connections": { - "input_bams_0|input_bam": { - "id": 11, - "output_name": "outFile" - }, - "reference_source|ref_file": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Freebayes4Workflow", - "outputs": [ - { - "name": "output_vcf_default", - "type": "vcf" - }, - { - "name": "output_vcf_firstBAM", - "type": "vcf" - }, - { - "name": "output_vcf_rename", - "type": "vcf" - }, - { - "name": "output_failed_alleles_bed", - "type": "bed" - }, - { - "name": "output_trace", - "type": "txt" - } - ], - "position": { - "left": 1545, - "top": 1195 - }, - "post_job_actions": { - "HideDatasetActionoutput_failed_alleles_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_failed_alleles_bed" - }, - "HideDatasetActionoutput_trace": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_trace" - }, - "HideDatasetActionoutput_vcf_default": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_default" - }, - "HideDatasetActionoutput_vcf_firstBAM": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_firstBAM" - }, - "HideDatasetActionoutput_vcf_rename": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_vcf_rename" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", - "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", - "tool_version": "0.5", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "", - "id": 15, - "input_connections": { - "input1": { - "id": 11, - "output_name": "outFile" - } - }, - "inputs": [], - "name": "flagstat", - "outputs": [ - { - "name": "output1", - "type": "txt" - } - ], - "position": { - "left": 1411, - "top": 1770 - }, - "post_job_actions": { - "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output1" - }, - "RenameDatasetActionoutput1": { - "action_arguments": { - "newname": "#{inupt1| basename}.stats" - }, - "action_type": "RenameDatasetAction", - "output_name": "output1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "16": { - "annotation": "", - "id": 16, - "input_connections": { - "BedFile_List|BedFiles_0|inputBed": { - "id": 6, - "output_name": "output_bed" - }, - "inputVCF": { - "id": 12, - "output_name": "output_vcf_firstBAM" - } - }, - "inputs": [], - "name": "VCFFiltering", - "outputs": [ - { - "name": "outputVCF", - "type": "vcf" - }, - { - "name": "output_html", - "type": "html" - } - ], - "position": { - "left": 1739, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionoutputVCF": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outputVCF" - }, - "HideDatasetActionoutput_html": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_html" - }, - "RenameDatasetActionoutputVCF": { - "action_arguments": { - "newname": "#{inputVCF | basename}.filteredVCF" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCF" - }, - "RenameDatasetActionoutput_html": { - "action_arguments": { - "newname": "#{inputVCF | basename}.VCFFiltering.graphs" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_html" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", - "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "17": { - "annotation": "", - "id": 17, - "input_connections": { - "BedFile_List|BedFiles_0|inputBed": { - "id": 6, - "output_name": "output_bed" - }, - "inputVCF": { - "id": 14, - "output_name": "output_vcf_firstBAM" - } - }, - "inputs": [], - "name": "VCFFiltering", - "outputs": [ - { - "name": "outputVCF", - "type": "vcf" - }, - { - "name": "output_html", - "type": "html" - } - ], - "position": { - "left": 1739, - "top": 778 - }, - "post_job_actions": { - "HideDatasetActionoutputVCF": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outputVCF" - }, - "HideDatasetActionoutput_html": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_html" - }, - "RenameDatasetActionoutputVCF": { - "action_arguments": { - "newname": "#{inputVCF | basename}.filteredVCF" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCF" - }, - "RenameDatasetActionoutput_html": { - "action_arguments": { - "newname": "#{inputVCF | basename}.VCFFiltering.graphs" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_html" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", - "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "18": { - "annotation": "", - "id": 18, - "input_connections": { - "VCFFile_0|inputStrainVCF": { - "id": 16, - "output_name": "outputVCF" - }, - "VCFFile_1|inputStrainVCF": { - "id": 17, - "output_name": "outputVCF" - }, - "inputFasta": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "VCFStorage", - "outputs": [ - { - "name": "outputVCFStorage", - "type": "tabular" - } - ], - "position": { - "left": 2067, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionoutputVCFStorage": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outputVCFStorage" - }, - "RenameDatasetActionoutputVCFStorage": { - "action_arguments": { - "newname": "#{inputFasta | basename}.matrix" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCFStorage" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", - "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"VCFFile\": \"[{\\\"strainName\\\": \\\"strain1\\\", \\\"__index__\\\": 0, \\\"inputStrainVCF\\\": null}, {\\\"strainName\\\": \\\"strain2\\\", \\\"__index__\\\": 1, \\\"inputStrainVCF\\\": null}]\", \"inputFasta\": \"null\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "19": { - "annotation": "", - "id": 19, - "input_connections": { - "inputTabular": { - "id": 18, - "output_name": "outputVCFStorage" - } - }, - "inputs": [], - "name": "VCFCarto", - "outputs": [ - { - "name": "outputVCFCarto", - "type": "tabular" - }, - { - "name": "output_html", - "type": "html" - }, - { - "name": "output_bed", - "type": "bed" - } - ], - "position": { - "left": 2387, - "top": 593 - }, - "post_job_actions": { - "HideDatasetActionoutput_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_bed" - }, - "HideDatasetActionoutput_html": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_html" - }, - "RenameDatasetActionoutputVCFCarto": { - "action_arguments": { - "newname": "#{inputTabular | basename}.red" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputVCFCarto" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01", - "tool_state": "{\"__page__\": 0, \"parentA\": \"\\\"strain1\\\"\", \"__rerun_remap_job_id__\": null, \"outputType\": \"\\\"raw\\\"\", \"parentH\": \"\\\"strain2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputTabular\": \"null\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - } - }, - "uuid": "359c9c1b-1771-475c-b353-1b9a0d802f18" -}