Mercurial > repos > urgi-team > gandalfworkflow
changeset 2:cfc5177134ce draft
Uploaded
| author | urgi-team |
|---|---|
| date | Wed, 18 Nov 2015 09:14:53 -0500 |
| parents | 95efdc025a48 |
| children | 025efd59ddd0 |
| files | Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Galaxy-Workflow-workflow_gandalf_1.0.ga Galaxy-Workflow-workflow_gandalf_3.0.ga repository_dependencies.xml |
| diffstat | 4 files changed, 601 insertions(+), 596 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Wed Nov 18 09:14:53 2015 -0500 @@ -0,0 +1,384 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "creation workflow gandalf 2.0", + "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" +} \ No newline at end of file
--- a/Galaxy-Workflow-workflow_gandalf_1.0.ga Thu Nov 12 07:40:16 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
--- a/Galaxy-Workflow-workflow_gandalf_3.0.ga Thu Nov 12 07:40:16 2015 -0500 +++ b/Galaxy-Workflow-workflow_gandalf_3.0.ga Wed Nov 18 09:14:53 2015 -0500 @@ -18,7 +18,7 @@ "outputs": [], "position": { "left": 258, - "top": 260 + "top": 593 }, "tool_errors": null, "tool_id": null, @@ -41,7 +41,7 @@ "outputs": [], "position": { "left": 258, - "top": 352 + "top": 685 }, "tool_errors": null, "tool_id": null, @@ -64,7 +64,7 @@ "outputs": [], "position": { "left": 252, - "top": 440 + "top": 773 }, "tool_errors": null, "tool_id": null, @@ -87,7 +87,7 @@ "outputs": [], "position": { "left": 241, - "top": 520 + "top": 853 }, "tool_errors": null, "tool_id": null, @@ -110,7 +110,7 @@ "outputs": [], "position": { "left": 245, - "top": 605 + "top": 938 }, "tool_errors": null, "tool_id": null, @@ -123,6 +123,56 @@ "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" @@ -145,8 +195,8 @@ } ], "position": { - "left": 527, - "top": 260 + "left": 1188, + "top": 230 }, "post_job_actions": { "HideDatasetActionoutput_bed": { @@ -179,121 +229,11 @@ "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": 527, - "top": 428 - }, - "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__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"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": 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": 596 - }, - "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": [] - }, - "8": { - "annotation": "", - "id": 8, - "input_connections": { - "fastq_input|fastq_input1": { "id": 3, "output_name": "output" }, @@ -316,7 +256,7 @@ ], "position": { "left": 527, - "top": 781 + "top": 1114 }, "post_job_actions": { "HideDatasetActionbam_output": { @@ -339,12 +279,12 @@ "type": "tool", "user_outputs": [] }, - "9": { + "8": { "annotation": "", - "id": 9, + "id": 8, "input_connections": { "input1": { - "id": 7, + "id": 5, "output_name": "bam_output" } }, @@ -358,7 +298,7 @@ ], "position": { "left": 855, - "top": 260 + "top": 593 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -381,12 +321,12 @@ "type": "tool", "user_outputs": [] }, - "10": { + "9": { "annotation": "", - "id": 10, + "id": 9, "input_connections": { "input1": { - "id": 8, + "id": 7, "output_name": "bam_output" } }, @@ -400,7 +340,7 @@ ], "position": { "left": 855, - "top": 373 + "top": 706 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -423,12 +363,12 @@ "type": "tool", "user_outputs": [] }, - "11": { + "10": { "annotation": "", - "id": 11, + "id": 10, "input_connections": { "inputFile": { - "id": 9, + "id": 8, "output_name": "output1" } }, @@ -446,7 +386,7 @@ ], "position": { "left": 1083, - "top": 260 + "top": 593 }, "post_job_actions": { "HideDatasetActionmetrics_file": { @@ -474,12 +414,12 @@ "type": "tool", "user_outputs": [] }, - "12": { + "11": { "annotation": "", - "id": 12, + "id": 11, "input_connections": { "inputFile": { - "id": 10, + "id": 9, "output_name": "output1" } }, @@ -497,7 +437,7 @@ ], "position": { "left": 1083, - "top": 418 + "top": 751 }, "post_job_actions": { "HideDatasetActionmetrics_file": { @@ -525,10 +465,127 @@ "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" @@ -563,125 +620,8 @@ } ], "position": { - "left": 1411, - "top": 260 - }, - "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": [] - }, - "14": { - "annotation": "", - "id": 14, - "input_connections": { - "input1": { - "id": 11, - "output_name": "outFile" - } - }, - "inputs": [], - "name": "flagstat", - "outputs": [ - { - "name": "output1", - "type": "txt" - } - ], - "position": { - "left": 1411, - "top": 792 - }, - "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": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "", - "id": 15, - "input_connections": { - "input_bams_0|input_bam": { - "id": 12, - "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": 862 + "top": 1195 }, "post_job_actions": { "HideDatasetActionoutput_failed_alleles_bed": { @@ -717,12 +657,12 @@ "type": "tool", "user_outputs": [] }, - "16": { + "15": { "annotation": "", - "id": 16, + "id": 15, "input_connections": { "input1": { - "id": 12, + "id": 11, "output_name": "outFile" } }, @@ -736,7 +676,7 @@ ], "position": { "left": 1411, - "top": 1437 + "top": 1770 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -755,20 +695,20 @@ "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": "1.0.0", + "tool_version": "1.0.1", "type": "tool", "user_outputs": [] }, - "17": { + "16": { "annotation": "", - "id": 17, + "id": 16, "input_connections": { "BedFile_List|BedFiles_0|inputBed": { "id": 6, "output_name": "output_bed" }, "inputVCF": { - "id": 13, + "id": 12, "output_name": "output_vcf_firstBAM" } }, @@ -786,7 +726,7 @@ ], "position": { "left": 1739, - "top": 260 + "top": 593 }, "post_job_actions": { "HideDatasetActionoutputVCF": { @@ -821,16 +761,16 @@ "type": "tool", "user_outputs": [] }, - "18": { + "17": { "annotation": "", - "id": 18, + "id": 17, "input_connections": { "BedFile_List|BedFiles_0|inputBed": { - "id": 5, + "id": 6, "output_name": "output_bed" }, "inputVCF": { - "id": 15, + "id": 14, "output_name": "output_vcf_firstBAM" } }, @@ -848,7 +788,7 @@ ], "position": { "left": 1739, - "top": 445 + "top": 778 }, "post_job_actions": { "HideDatasetActionoutputVCF": { @@ -883,16 +823,16 @@ "type": "tool", "user_outputs": [] }, - "19": { + "18": { "annotation": "", - "id": 19, + "id": 18, "input_connections": { "VCFFile_0|inputStrainVCF": { - "id": 17, + "id": 16, "output_name": "outputVCF" }, "VCFFile_1|inputStrainVCF": { - "id": 18, + "id": 17, "output_name": "outputVCF" }, "inputFasta": { @@ -910,7 +850,7 @@ ], "position": { "left": 2067, - "top": 260 + "top": 593 }, "post_job_actions": { "HideDatasetActionoutputVCFStorage": { @@ -933,12 +873,12 @@ "type": "tool", "user_outputs": [] }, - "20": { + "19": { "annotation": "", - "id": 20, + "id": 19, "input_connections": { "inputTabular": { - "id": 19, + "id": 18, "output_name": "outputVCFStorage" } }, @@ -960,7 +900,7 @@ ], "position": { "left": 2387, - "top": 260 + "top": 593 }, "post_job_actions": { "HideDatasetActionoutput_bed": { @@ -989,5 +929,5 @@ "user_outputs": [] } }, - "uuid": "7924e8b4-f601-4a2e-a768-203f86c4f94e" + "uuid": "359c9c1b-1771-475c-b353-1b9a0d802f18" } \ No newline at end of file
--- a/repository_dependencies.xml Thu Nov 12 07:40:16 2015 -0500 +++ b/repository_dependencies.xml Wed Nov 18 09:14:53 2015 -0500 @@ -6,4 +6,5 @@ <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="3552a8d9f51c" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="af65bfb54977" name="suite_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="cc6db1ee2d48" name="mdust" owner=" urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>