Mercurial > repos > bgruening > deeptools
view Galaxy-Workflow-2_BAM_files_--_(clustered)_Heatmap_of_read_coverages.ga @ 25:d2898b81b912 draft
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author | bgruening |
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date | Tue, 04 Feb 2014 13:45:17 -0500 |
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{ "a_galaxy_workflow": "true", "annotation": "Normalizes 2 BAM files to each other (log2ratio of BAM-file 1 / BAM file 2). Then generates a heatmap for regions supplied in 1 BED file (clustering possible). Output: bigWig file, computeMatrix table, heatmapper image", "format-version": "0.1", "name": "2 BAM files -->(clustered) Heatmap of read coverages", "steps": { "0": { "annotation": "sorted BAM file", "id": 0, "input_connections": {}, "inputs": [ { "description": "sorted BAM file", "name": "file 1 of mapped reads, e.g. treated sample" } ], "name": "Input dataset", "outputs": [], "position": { "left": 257.5, "top": 480 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"file 1 of mapped reads, e.g. treated sample\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "BED or INTERVAL file of genome regions to plot the read coverage for", "id": 1, "input_connections": {}, "inputs": [ { "description": "BED or INTERVAL file of genome regions to plot the read coverage for", "name": "regions" } ], "name": "Input dataset", "outputs": [], "position": { "left": 590.5, "top": 239 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"regions\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "sorted BAM file", "id": 2, "input_connections": {}, "inputs": [ { "description": "sorted BAM file", "name": "file 2 of mapped reads, e.g. control sample" } ], "name": "Input dataset", "outputs": [], "position": { "left": 276.5, "top": 594.5 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"file 2 of mapped reads, e.g. control sample\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "3": { "annotation": "generates a normalized coverage file (bigWig format)", "id": 3, "input_connections": { "bamFile1": { "id": 0, "output_name": "output" }, "bamFile2": { "id": 2, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool bamCompare", "name": "region" }, { "description": "runtime parameter for tool bamCompare", "name": "advancedOpt" }, { "description": "runtime parameter for tool bamCompare", "name": "fragmentLength" } ], "name": "bamCompare", "outputs": [ { "name": "outFileName", "type": "bigwig" } ], "position": { "left": 476.5, "top": 486.5 }, "post_job_actions": { "HideDatasetActionoutFileName": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileName" }, "RenameDatasetActionoutFileName": { "action_arguments": { "newname": "BAM1_vs_BAM2_log2ratio.bigwig" }, "action_type": "RenameDatasetAction", "output_name": "outFileName" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCompare/1.0.4", "tool_state": "{\"comparison\": \"{\\\"type\\\": \\\"log2\\\", \\\"__current_case__\\\": 0}\", \"bamFile2\": \"null\", \"outFileFormat\": \"\\\"bigwig\\\"\", \"bamFile1\": \"null\", \"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"binSize\": \"\\\"50\\\"\", \"scaling\": \"{\\\"method\\\": \\\"readCount\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advancedOpt\": \"{\\\"ignoreDuplicates\\\": \\\"True\\\", \\\"ignoreForNormalization\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"doNotExtendPairedEnds\\\": \\\"False\\\", \\\"missingDataAsZero\\\": \\\"True\\\", \\\"smoothLength\\\": \\\"150\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"minMappingQuality\\\": \\\"10\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "regionsFiles_0|regionsFile": { "id": 1, "output_name": "output" }, "scoreFile": { "id": 3, "output_name": "outFileName" } }, "inputs": [], "name": "computeMatrix", "outputs": [ { "name": "outFileName", "type": "bgzip" }, { "name": "outFileNameData", "type": "tabular" }, { "name": "outFileSortedRegions", "type": "bed" }, { "name": "outFileNameMatrix", "type": "tabular" } ], "position": { "left": 835.61669921875, "top": 364.1166687011719 }, "post_job_actions": { "HideDatasetActionoutFileNameData": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileNameData" }, "HideDatasetActionoutFileNameMatrix": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileNameMatrix" }, "HideDatasetActionoutFileSortedRegions": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileSortedRegions" }, "RenameDatasetActionoutFileName": { "action_arguments": { "newname": "computeMatrix: matrix of coverage values for BED file" }, "action_type": "RenameDatasetAction", "output_name": "outFileName" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.4", "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"startLabel\\\": \\\"TSS\\\", \\\"regionStartLength\\\": {\\\"afterRegionStartLength\\\": \\\"1000\\\", \\\"regionStartLength_select\\\": \\\"yes\\\", \\\"beforeRegionStartLength\\\": \\\"1000\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"endLabel\\\": \\\"TES\\\", \\\"regionBodyLength\\\": \\\"2000\\\", \\\"mode_select\\\": \\\"scale-regions\\\"}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] }, "5": { "annotation": "create a heatmap, if wanted, kmeans clustering can be performed", "id": 5, "input_connections": { "matrixFile": { "id": 4, "output_name": "outFileName" } }, "inputs": [ { "description": "runtime parameter for tool heatmapper", "name": "output" }, { "description": "runtime parameter for tool heatmapper", "name": "advancedOpt" }, { "description": "runtime parameter for tool heatmapper", "name": "advancedOpt" }, { "description": "runtime parameter for tool heatmapper", "name": "advancedOpt" }, { "description": "runtime parameter for tool heatmapper", "name": "advancedOpt" }, { "description": "runtime parameter for tool heatmapper", "name": "advancedOpt" } ], "name": "heatmapper", "outputs": [ { "name": "outFileName", "type": "png" }, { "name": "outFileNameData", "type": "tabular" }, { "name": "outFileSortedRegions", "type": "bed" }, { "name": "outFileNameMatrix", "type": "tabular" } ], "position": { "left": 1144.5, "top": 397 }, "post_job_actions": { "HideDatasetActionoutFileNameData": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileNameData" }, "HideDatasetActionoutFileNameMatrix": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileNameMatrix" }, "HideDatasetActionoutFileSortedRegions": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileSortedRegions" }, "RenameDatasetActionoutFileName": { "action_arguments": { "newname": "Heatmap of treatment_control_log2ratios" }, "action_type": "RenameDatasetAction", "output_name": "outFileName" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.4", "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] } } }