Mercurial > repos > sanbi-uwc > sanbi_freebayes_variant_calling
view SANBI_freebayes_variant_call.ga @ 0:31dec9fabb7e draft default tip
planemo upload for repository https://github.com/SANBI-SA/freebayes_variant_calling.git commit acb732ca27d8a957edb5097fd540a317e44aa6b5
| author | sanbi-uwc |
|---|---|
| date | Wed, 08 Feb 2017 04:53:24 -0500 |
| parents | |
| children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Latest 'Zahra - Freebase Workflow'", "steps": { "0": { "annotation": "", "content_id": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset Collection" } ], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 200, "top": 200 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", "tool_version": null, "type": "data_collection_input", "uuid": "ec0eca4d-883c-46ef-a904-2bada2f0c223", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "19ad0e5f-bbf9-49f2-bfb6-e894ce87b014" } ] }, "1": { "annotation": "", "content_id": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 285.5 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "uuid": "393c1a33-7710-49ee-bb5a-af8829360a25", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "297f8893-ecc5-41f8-84c9-470ad6d12759" } ] }, "2": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/trimmomatic/trimmomatic/0.36.2", "id": 2, "input_connections": { "readtype|fastq_pair": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Trimmomatic", "name": "readtype" } ], "label": null, "name": "Trimmomatic", "outputs": [ { "name": "fastq_out_paired", "type": "input" }, { "name": "fastq_out_unpaired", "type": "input" }, { "name": "fastq_out_r1_paired", "type": "input" }, { "name": "fastq_out_r2_paired", "type": "input" }, { "name": "fastq_out_r1_unpaired", "type": "input" }, { "name": "fastq_out_r2_unpaired", "type": "input" }, { "name": "fastq_out", "type": "input" } ], "position": { "left": 473.5, "top": 200 }, "post_job_actions": { "HideDatasetActionfastq_out": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out" }, "HideDatasetActionfastq_out_paired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_paired" }, "HideDatasetActionfastq_out_r1_paired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_r1_paired" }, "HideDatasetActionfastq_out_r1_unpaired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_r1_unpaired" }, "HideDatasetActionfastq_out_r2_paired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_r2_paired" }, "HideDatasetActionfastq_out_r2_unpaired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_r2_unpaired" }, "HideDatasetActionfastq_out_unpaired": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastq_out_unpaired" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/trimmomatic/trimmomatic/0.36.2", "tool_shed_repository": { "changeset_revision": "5c5a2a7e9cbb", "name": "trimmomatic", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"collection\\\", \\\"fastq_pair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", "tool_version": "0.36.2", "type": "tool", "uuid": "f06a1a6e-8919-470d-af36-59f501360471", "workflow_outputs": [] }, "3": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/novo_align/novo_align/0.0.7", "id": 3, "input_connections": { "index|reference": { "id": 1, "output_name": "output" }, "paired_end|paired_input_type_conditional|fastq_pair": { "id": 2, "output_name": "fastq_out_paired" } }, "inputs": [ { "description": "runtime parameter for tool NOVO ALIGN", "name": "index" } ], "label": null, "name": "NOVO ALIGN", "outputs": [ { "name": "out_file", "type": "bam" } ], "position": { "left": 801, "top": 200 }, "post_job_actions": { "HideDatasetActionout_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/novo_align/novo_align/0.0.7", "tool_shed_repository": { "changeset_revision": "b8fd92de9062", "name": "novo_align", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"index\": \"{\\\"source\\\": \\\"history\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"true\\\", \\\"paired_input_type_conditional\\\": {\\\"fastq_pair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_input_type\\\": \\\"collection\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1}\", \"__page__\": 0}", "tool_version": "0.0.7", "type": "tool", "uuid": "1f63736d-0cf4-49d0-bca7-218941f484ca", "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/novo_sort/novo_sort/0.0.2", "id": 4, "input_connections": { "input1": { "id": 3, "output_name": "out_file" } }, "inputs": [ { "description": "runtime parameter for tool NOVO SORT", "name": "input1" } ], "label": null, "name": "NOVO SORT", "outputs": [ { "name": "out_file", "type": "bam" } ], "position": { "left": 1128.5, "top": 200 }, "post_job_actions": { "HideDatasetActionout_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/novo_sort/novo_sort/0.0.2", "tool_shed_repository": { "changeset_revision": "2f3d4c867e1d", "name": "novo_sort", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.0.2", "type": "tool", "uuid": "ae4f13bb-f6df-4a91-9166-8fbc2be31cb0", "workflow_outputs": [] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_MarkDuplicates/1.135", "id": 5, "input_connections": { "inputFile": { "id": 4, "output_name": "out_file" } }, "inputs": [ { "description": "runtime parameter for tool MarkDuplicates", "name": "inputFile" } ], "label": null, "name": "MarkDuplicates", "outputs": [ { "name": "metrics_file", "type": "txt" }, { "name": "outFile", "type": "bam" } ], "position": { "left": 1356, "top": 200 }, "post_job_actions": { "HideDatasetActionmetrics_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "metrics_file" }, "HideDatasetActionoutFile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_MarkDuplicates/1.135", "tool_shed_repository": { "changeset_revision": "5f1da1eadb39", "name": "picard", "owner": "avowinkel", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"false\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"true\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.135", "type": "tool", "uuid": "8836dc40-a7db-46cc-9efc-e1e2cd54afb8", "workflow_outputs": [] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_CASM/1.135", "id": 6, "input_connections": { "inputFile": { "id": 4, "output_name": "out_file" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Collect Alignment Summary Metrics", "name": "reference_source" }, { "description": "runtime parameter for tool Collect Alignment Summary Metrics", "name": "inputFile" } ], "label": null, "name": "Collect Alignment Summary Metrics", "outputs": [ { "name": "outFile", "type": "tabular" } ], "position": { "left": 1356, "top": 368.5 }, "post_job_actions": { "HideDatasetActionoutFile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_CASM/1.135", "tool_shed_repository": { "changeset_revision": "5f1da1eadb39", "name": "picard", "owner": "avowinkel", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bisulphite\": \"\\\"false\\\"\", \"__page__\": 0, \"maxinsert\": \"\\\"100000\\\"\", \"__rerun_remap_job_id__\": null, \"assume_sorted\": \"\\\"true\\\"\", \"metric_accumulation_level\": \"[\\\"ALL_READS\\\"]\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"adapters\": \"[]\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.135", "type": "tool", "uuid": "4a3c1f72-ecd9-469d-9067-663077904732", "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.1", "id": 7, "input_connections": { "reference_source|input_bam": { "id": 5, "output_name": "outFile" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Realigner Target Creator", "name": "reference_source" }, { "description": "runtime parameter for tool Realigner Target Creator", "name": "reference_source" } ], "label": null, "name": "Realigner Target Creator", "outputs": [ { "name": "output_interval", "type": "gatk_interval" }, { "name": "output_log", "type": "txt" } ], "position": { "left": 1683.5, "top": 200 }, "post_job_actions": { "HideDatasetActionoutput_interval": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval" }, "HideDatasetActionoutput_log": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_log" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.1", "tool_shed_repository": { "changeset_revision": "a3247b69fa59", "name": "gatk2", "owner": "iuc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bam\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"allow_n_cigar_reads\": \"\\\"false\\\"\", \"rod_bind\": \"[]\"}", "tool_version": "2.8.1", "type": "tool", "uuid": "953784c8-a946-4062-b357-e857b17c9d86", "workflow_outputs": [] }, "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_CASM/1.135", "id": 8, "input_connections": { "inputFile": { "id": 5, "output_name": "outFile" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Collect Alignment Summary Metrics", "name": "reference_source" }, { "description": "runtime parameter for tool Collect Alignment Summary Metrics", "name": "inputFile" } ], "label": null, "name": "Collect Alignment Summary Metrics", "outputs": [ { "name": "outFile", "type": "tabular" } ], "position": { "left": 1683.5, "top": 395.5 }, "post_job_actions": { "HideDatasetActionoutFile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_CASM/1.135", "tool_shed_repository": { "changeset_revision": "5f1da1eadb39", "name": "picard", "owner": "avowinkel", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"bisulphite\": \"\\\"false\\\"\", \"__page__\": 0, \"maxinsert\": \"\\\"100000\\\"\", \"__rerun_remap_job_id__\": null, \"assume_sorted\": \"\\\"true\\\"\", \"metric_accumulation_level\": \"[\\\"ALL_READS\\\"]\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"adapters\": \"[]\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.135", "type": "tool", "uuid": "0ce4816e-6b77-4613-ace6-dc3d17449930", "workflow_outputs": [] }, "9": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.1", "id": 9, "input_connections": { "reference_source|input_bam": { "id": 5, "output_name": "outFile" }, "reference_source|ref_file": { "id": 1, "output_name": "output" }, "target_intervals": { "id": 7, "output_name": "output_interval" } }, "inputs": [ { "description": "runtime parameter for tool Indel Realigner", "name": "target_intervals" }, { "description": "runtime parameter for tool Indel Realigner", "name": "reference_source" }, { "description": "runtime parameter for tool Indel Realigner", "name": "reference_source" } ], "label": null, "name": "Indel Realigner", "outputs": [ { "name": "output_bam", "type": "bam" }, { "name": "output_log", "type": "txt" } ], "position": { "left": 2011, "top": 200 }, "post_job_actions": { "HideDatasetActionoutput_bam": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_bam" }, "HideDatasetActionoutput_log": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_log" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.1", "tool_shed_repository": { "changeset_revision": "a3247b69fa59", "name": "gatk2", "owner": "iuc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"false\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bam\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"allow_n_cigar_reads\": \"\\\"false\\\"\", \"rod_bind\": \"[]\"}", "tool_version": "2.8.1", "type": "tool", "uuid": "540efb47-4d82-4204-b15b-f41449b676cf", "workflow_outputs": [] }, "10": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.1", "id": 10, "input_connections": { "reference_source|input_bams": { "id": 9, "output_name": "output_bam" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Depth of Coverage", "name": "input_calculate_coverage_over_genes" }, { "description": "runtime parameter for tool Depth of Coverage", "name": "reference_source" }, { "description": "runtime parameter for tool Depth of Coverage", "name": "reference_source" } ], "label": null, "name": "Depth of Coverage", "outputs": [ { "name": "output_per_locus_coverage", "type": "tabular" }, { "name": "output_summary_sample", "type": "tabular" }, { "name": "output_statistics_sample", "type": "tabular" }, { "name": "output_interval_summary_sample", "type": "tabular" }, { "name": "output_interval_statistics_sample", "type": "tabular" }, { "name": "output_gene_summary_sample", "type": "tabular" }, { "name": "output_gene_statistics_sample", "type": "tabular" }, { "name": "output_cumulative_coverage_counts_sample", "type": "tabular" }, { "name": "output_cumulative_coverage_proportions_sample", "type": "tabular" }, { "name": "output_summary_readgroup", "type": "tabular" }, { "name": "output_statistics_readgroup", "type": "tabular" }, { "name": "output_interval_summary_readgroup", "type": "tabular" }, { "name": "output_interval_statistics_readgroup", "type": "tabular" }, { "name": "output_gene_summary_readgroup", "type": "tabular" }, { "name": "output_gene_statistics_readgroup", "type": "tabular" }, { "name": "output_cumulative_coverage_counts_readgroup", "type": "tabular" }, { "name": "output_cumulative_coverage_proportions_readgroup", "type": "tabular" }, { "name": "output_summary_library", "type": "tabular" }, { "name": "output_statistics_library", "type": "tabular" }, { "name": "output_interval_summary_library", "type": "tabular" }, { "name": "output_interval_statistics_library", "type": "tabular" }, { "name": "output_gene_summary_library", "type": "tabular" }, { "name": "output_gene_statistics_library", "type": "tabular" }, { "name": "output_cumulative_coverage_counts_library", "type": "tabular" }, { "name": "output_cumulative_coverage_proportions_library", "type": "tabular" }, { "name": "output_log", "type": "tabular" } ], "position": { "left": 2338.5, "top": 200 }, "post_job_actions": { "HideDatasetActionoutput_cumulative_coverage_counts_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_counts_library" }, "HideDatasetActionoutput_cumulative_coverage_counts_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_counts_readgroup" }, "HideDatasetActionoutput_cumulative_coverage_counts_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_counts_sample" }, "HideDatasetActionoutput_cumulative_coverage_proportions_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_proportions_library" }, "HideDatasetActionoutput_cumulative_coverage_proportions_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_proportions_readgroup" }, "HideDatasetActionoutput_cumulative_coverage_proportions_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cumulative_coverage_proportions_sample" }, "HideDatasetActionoutput_gene_statistics_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_statistics_library" }, "HideDatasetActionoutput_gene_statistics_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_statistics_readgroup" }, "HideDatasetActionoutput_gene_statistics_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_statistics_sample" }, "HideDatasetActionoutput_gene_summary_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_summary_library" }, "HideDatasetActionoutput_gene_summary_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_summary_readgroup" }, "HideDatasetActionoutput_gene_summary_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_gene_summary_sample" }, "HideDatasetActionoutput_interval_statistics_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_statistics_library" }, "HideDatasetActionoutput_interval_statistics_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_statistics_readgroup" }, "HideDatasetActionoutput_interval_statistics_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_statistics_sample" }, "HideDatasetActionoutput_interval_summary_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_summary_library" }, "HideDatasetActionoutput_interval_summary_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_summary_readgroup" }, "HideDatasetActionoutput_interval_summary_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_interval_summary_sample" }, "HideDatasetActionoutput_log": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_log" }, "HideDatasetActionoutput_per_locus_coverage": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_per_locus_coverage" }, "HideDatasetActionoutput_statistics_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_statistics_library" }, "HideDatasetActionoutput_statistics_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_statistics_readgroup" }, "HideDatasetActionoutput_statistics_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_statistics_sample" }, "HideDatasetActionoutput_summary_library": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_summary_library" }, "HideDatasetActionoutput_summary_readgroup": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_summary_readgroup" }, "HideDatasetActionoutput_summary_sample": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_summary_sample" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.1", "tool_shed_repository": { "changeset_revision": "a3247b69fa59", "name": "gatk2", "owner": "iuc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"summary_coverage_threshold_group\": \"[]\", \"__page__\": 0, \"output_format\": \"\\\"rtable\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_calculate_coverage_over_genes\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"partition_type\": \"[\\\"sample\\\"]\"}", "tool_version": "2.8.1", "type": "tool", "uuid": "fcd1e16b-6a8d-4c4f-8b0a-b489c27f0518", "workflow_outputs": [] }, "11": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4.1", "id": 11, "input_connections": { "reference_source|input_bams_0|input_bam": { "id": 9, "output_name": "output_bam" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool FreeBayes", "name": "reference_source" } ], "label": null, "name": "FreeBayes", "outputs": [ { "name": "output_vcf", "type": "vcf" }, { "name": "output_failed_alleles_bed", "type": "bed" }, { "name": "output_trace", "type": "txt" } ], "position": { "left": 2338.5, "top": 1321.5 }, "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": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_vcf" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4.1", "tool_shed_repository": { "changeset_revision": "9f3d6c3098ac", "name": "freebayes", "owner": "devteam", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}], \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"simple\\\"}\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "0.4.1", "type": "tool", "uuid": "35f61b4a-76ad-42e9-8056-e2c0731d5eda", "workflow_outputs": [] }, "12": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/qualimap2/qualimap_bamqc/2.2", "id": 12, "input_connections": { "input_realigned_bam_file": { "id": 9, "output_name": "output_bam" } }, "inputs": [ { "description": "runtime parameter for tool QualiMap BamQC", "name": "input_realigned_bam_file" } ], "label": null, "name": "QualiMap BamQC", "outputs": [ { "name": "genomecov_file", "type": "genomecov" } ], "position": { "left": 2338.5, "top": 1548 }, "post_job_actions": { "HideDatasetActiongenomecov_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "genomecov_file" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/qualimap2/qualimap_bamqc/2.2", "tool_shed_repository": { "changeset_revision": "7923e67fa16a", "name": "qualimap2", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"mem_size\": \"\\\"8G\\\"\", \"__rerun_remap_job_id__\": null, \"input_realigned_bam_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", "tool_version": "2.2", "type": "tool", "uuid": "88e90561-cd29-4f89-8e2d-25e283baf919", "workflow_outputs": [] }, "13": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/4.1.0", "id": 13, "input_connections": { "input": { "id": 11, "output_name": "output_vcf" } }, "inputs": [ { "description": "runtime parameter for tool SnpEff", "name": "intervals" }, { "description": "runtime parameter for tool SnpEff", "name": "input" }, { "description": "runtime parameter for tool SnpEff", "name": "transcripts" } ], "label": null, "name": "SnpEff", "outputs": [ { "name": "snpeff_output", "type": "vcf" }, { "name": "statsFile", "type": "html" } ], "position": { "left": 2666, "top": 200 }, "post_job_actions": { "HideDatasetActionstatsFile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "statsFile" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/4.1.0", "tool_shed_repository": { "changeset_revision": "924af057bbca", "name": "snpeff", "owner": "jjohnson", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"spliceSiteSize\": \"\\\"2\\\"\", \"filter\": \"{\\\"specificEffects\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"filterOut\": \"null\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputFormat\": \"\\\"vcf\\\"\", \"__page__\": 0, \"outputConditional\": \"{\\\"outputFormat\\\": \\\"vcf\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"udLength\": \"\\\"5000\\\"\", \"generate_stats\": \"\\\"true\\\"\", \"noLog\": \"\\\"true\\\"\", \"chr\": \"\\\"\\\"\", \"intervals\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"snpDb\": \"{\\\"genome_version\\\": \\\"m_tuberculosis_H37Rv\\\", \\\"__current_case__\\\": 2, \\\"genomeSrc\\\": \\\"named\\\"}\", \"offset\": \"\\\"default\\\"\", \"spliceRegion\": \"{\\\"__current_case__\\\": 0, \\\"setSpliceRegions\\\": \\\"no\\\"}\", \"transcripts\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"annotations\": \"null\"}", "tool_version": "4.1.0", "type": "tool", "uuid": "d55dbcd4-0c43-4d8f-86e3-e4f2fee31121", "workflow_outputs": [ { "label": null, "output_name": "snpeff_output", "uuid": "78916445-9abd-447f-8ce2-b46d73c37329" } ] }, "14": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/vcf_to_alignment/vcf_to_alignment/0.3", "id": 14, "input_connections": { "reference|history": { "id": 1, "output_name": "output" }, "vcf_inputs": { "id": 13, "output_name": "snpeff_output" } }, "inputs": [ { "description": "runtime parameter for tool Generate FASTA alignment from VCF collection", "name": "reference" }, { "description": "runtime parameter for tool Generate FASTA alignment from VCF collection", "name": "vcf_inputs" } ], "label": null, "name": "Generate FASTA alignment from VCF collection", "outputs": [ { "name": "output_alignment", "type": "fasta" } ], "position": { "left": 2993.5, "top": 200 }, "post_job_actions": { "HideDatasetActionoutput_alignment": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_alignment" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/vcf_to_alignment/vcf_to_alignment/0.3", "tool_shed_repository": { "changeset_revision": "62fbd3f96b30", "name": "vcf_to_alignment", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"source\\\": \\\"history\\\", \\\"__current_case__\\\": 0, \\\"history\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"remove_invariant_sites\": \"\\\"false\\\"\", \"vcf_inputs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.3", "type": "tool", "uuid": "c3615be1-5772-4bbb-ae4c-3bad44d477f4", "workflow_outputs": [] }, "15": { "annotation": "", "content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/fasttree/fasttree/0.1", "id": 15, "input_connections": { "input_alignment": { "id": 14, "output_name": "output_alignment" } }, "inputs": [ { "description": "runtime parameter for tool FastTree", "name": "input_alignment" } ], "label": null, "name": "FastTree", "outputs": [ { "name": "output_tree", "type": "nhx" }, { "name": "output_log", "type": "txt" } ], "position": { "left": 3321, "top": 200 }, "post_job_actions": { "HideDatasetActionoutput_log": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_log" } }, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/fasttree/fasttree/0.1", "tool_shed_repository": { "changeset_revision": "614a12d56e58", "name": "fasttree", "owner": "sanbi-uwc", "tool_shed": "testtoolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"alignment_type1\\\": \\\"prot\\\", \\\"advanced_options_selector\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"input_alignment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.1", "type": "tool", "uuid": "cf360eb7-c003-485e-8825-010e4547263a", "workflow_outputs": [ { "label": null, "output_name": "output_tree", "uuid": "a69dad1e-2bde-4aa0-865a-730947306b12" } ] } }, "uuid": "9a0cb18d-9008-47b7-8930-bfb26238cf0c" }