# HG changeset patch # User getiria-onsongo # Date 1354816513 18000 # Node ID eeb3b7aa16d6601a3e26bd44fcc80603198fe854 # Parent 11c1341242d26f00b9933aa007dfad37a0843b1b Uploaded diff -r 11c1341242d2 -r eeb3b7aa16d6 BamExonCoverage1X10X20X30X.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BamExonCoverage1X10X20X30X.ga Thu Dec 06 12:55:13 2012 -0500 @@ -0,0 +1,450 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "BamExonCoverage1X10X20X30X", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "mapped reads: .BAM" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 197.4166259765625, + "top": 357.41667175292969 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"mapped reads: .BAM\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "targeted interval: .bed" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1202, + "top": 778 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"targeted interval: .bed\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "reference_source|input_bams_0|input_bam": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "MPileup", + "outputs": [ + { + "name": "output_mpileup", + "type": "pileup" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 454, + "top": 237 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "samtools_mpileup", + "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "output_mpileup" + } + }, + "inputs": [], + "name": "Compute", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 727, + "top": 372 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Add_a_column1", + "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2-1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"round\": \"\\\"yes\\\"\", \"input\": \"null\"}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "input": { + "id": 3, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 963, + "top": 322 + }, + "post_job_actions": { + "ChangeDatatypeActionout_file1": { + "action_arguments": { + "newtype": "interval" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c1,c7,c2,c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"__page__\": 0}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1184, + "top": 422 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 1\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "input1": { + "id": 1, + "output_name": "output" + }, + "input2": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Coverage", + "outputs": [ + { + "name": "output", + "type": "interval" + } + ], + "position": { + "left": 1485, + "top": 422 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "gops_coverage_1", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "input": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1439, + "top": 608 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 10\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input1": { + "id": 1, + "output_name": "output" + }, + "input2": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Coverage", + "outputs": [ + { + "name": "output", + "type": "interval" + } + ], + "position": { + "left": 1699, + "top": 614 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "gops_coverage_1", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "input": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1718, + "top": 773 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 20\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "input1": { + "id": 1, + "output_name": "output" + }, + "input2": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Coverage", + "outputs": [ + { + "name": "output", + "type": "interval" + } + ], + "position": { + "left": 1944, + "top": 773 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "gops_coverage_1", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "input": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1922, + "top": 976 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 30\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "input1": { + "id": 1, + "output_name": "output" + }, + "input2": { + "id": 11, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Coverage", + "outputs": [ + { + "name": "output", + "type": "interval" + } + ], + "position": { + "left": 2158, + "top": 977 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "gops_coverage_1", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "file_chooser_0|input": { + "id": 10, + "output_name": "output" + }, + "file_chooser_1|input": { + "id": 12, + "output_name": "output" + }, + "input1": { + "id": 6, + "output_name": "output" + }, + "input2": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "name": "Column Join", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 2387, + "top": 474 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Coverage1X10X20X30X" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "column_join", + "tool_state": "{\"input2\": \"null\", \"hinge\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"input1\": \"null\", \"__page__\": 0, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"file_chooser\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\", \\\"2\\\", \\\"3\\\", \\\"5\\\"]}\"}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file