Mercurial > repos > bgruening > deeptools_workflows
changeset 1:6f95aecbcad1 draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 03 Apr 2014 11:02:03 -0400 |
| parents | 3daf197399a2 |
| children | |
| files | 1_BAM_file_TO_Heatmap_of_read_coverages.ga 2_BAM_files_TO_clustered_Heatmap_of_read_coverages.ga Add_chr_to_first_column_of_a_6_columns_BED_file.ga Clustered_heatmap_of_signals_around_the_TSSs__1_bigWig_TO_heatmap.ga Compute_and_correct_GC_bias.ga Galaxy-Workflow-1_BAM_file_--_(clustered)_Heatmap_of_read_coverages.ga Galaxy-Workflow-2_BAM_files_--_(clustered)_Heatmap_of_read_coverages.ga Galaxy-Workflow-Add__chr__to_first_column_of_a_BED_file_(must_have_6_columns).ga Galaxy-Workflow-Clustered_heatmap_of_signals_around_the_TSSs.ga Galaxy-Workflow-Compute_and_correct_GC_bias.ga Remove_chr_from_the_beginning_of_genomic_interval_files.ga repository_dependencies.xml |
| diffstat | 12 files changed, 1120 insertions(+), 1052 deletions(-) [+] |
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--- a/Galaxy-Workflow-Add__chr__to_first_column_of_a_BED_file_(must_have_6_columns).ga Tue Feb 04 13:46:24 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "Add 'chr' to first column of a BED file (must have 6 columns)", - "steps": { - "0": { - "annotation": "The BED file MUST have 6 columns. Otherwise this workflow will fail.", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "The BED file MUST have 6 columns. Otherwise this workflow will fail.", - "name": "BED file" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 200, - "top": 193 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"BED file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": { - "input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Add column", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 423, - "top": 200 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "addValue", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "input1": { - "id": 1, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Merge Columns", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 657, - "top": 211 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "mergeCols1", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "input": { - "id": 2, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 872, - "top": 205 - }, - "post_job_actions": { - "ChangeDatatypeActionout_file1": { - "action_arguments": { - "newtype": "interval" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "out_file1" - }, - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "added \"chr\" to chromosome name" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Cut1", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", - "tool_version": "1.0.2", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- a/Galaxy-Workflow-Clustered_heatmap_of_signals_around_the_TSSs.ga Tue Feb 04 13:46:24 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,205 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "1 bigWig, 1 \nBED --> clustered heatmap", - "format-version": "0.1", - "name": "Clustered heatmap of signals around the TSSs", - "steps": { - "0": { - "annotation": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified", - "name": "Genes" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 175, - "top": 186.5 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Genes\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "must be in bigWig format, score can be anything: read coverages, GC content...", - 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"tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- a/Galaxy-Workflow-Compute_and_correct_GC_bias.ga Tue Feb 04 13:46:24 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "Compute and correct GC bias", - "steps": { - "0": { - "annotation": "must be a sorted BAM file", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "must be a sorted BAM file", - "name": "BAM file to be checked for GC bias" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 111, - "top": 420 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"BAM file to be checked for GC bias\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "**Computationall;y intensive**", - "id": 1, - "input_connections": { - "bamInput": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool computeGCBias", - "name": "region" - }, - { - "description": "runtime parameter for tool computeGCBias", - "name": "source" - }, - { - "description": "runtime parameter for tool computeGCBias", - "name": "effectiveGenomeSize" - }, - { - "description": "runtime parameter for tool computeGCBias", - "name": "image_format" - }, - { - "description": "runtime parameter for tool computeGCBias", - "name": "fragmentLength" - } - ], - "name": "computeGCBias", - "outputs": [ - { - "name": "outFileName", - "type": "tabular" - }, - { - "name": "outImageName", - "type": "png" - } - ], - "position": { - "left": 383.6166687011719, - "top": 270.1166687011719 - }, - "post_job_actions": { - "HideDatasetActionoutFileName": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outFileName" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/1.0.3", - "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"filterOut\\\": null, \\\"extraSampling\\\": null, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"sampleSize\\\": \\\"50000000\\\", \\\"__current_case__\\\": 1, \\\"regionSize\\\": \\\"300\\\"}\", \"image_format\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "GCbiasFrequenciesFile": { - "id": 1, - "output_name": "outFileName" - }, - "bamInput": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool correctGCBias", - "name": "region" - }, - { - "description": "runtime parameter for tool correctGCBias", - "name": "source" - }, - { - "description": "runtime parameter for tool correctGCBias", - "name": "effectiveGenomeSize" - } - ], - "name": "correctGCBias", - "outputs": [ - { - "name": "outFileName", - "type": "bam" - } - ], - "position": { - "left": 779.61669921875, - "top": 334.1166687011719 - }, - "post_job_actions": { - "RenameDatasetActionoutFileName": { - "action_arguments": { - "newname": "GCcorrected BAM file" - }, - "action_type": "RenameDatasetAction", - "output_name": "outFileName" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/1.0.3", - "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"GCbiasFrequenciesFile\": \"null\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"binSize\\\": \\\"50\\\"}\", \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Remove_chr_from_the_beginning_of_genomic_interval_files.ga Thu Apr 03 11:02:03 2014 -0400 @@ -0,0 +1,68 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Remove 'chr' from the beginning of genomic interval files", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "any column-based file of genomic intervals" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 268.5, + "top": 182.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"any column-based file of genomic intervals\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Trim", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 552, + "top": 168 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "removed \"chr\"" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "trimmer", + "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"end\": \"\\\"0\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"\\\"35\\\"\", \"start\": \"\\\"4\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"col\": \"\\\"1\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- a/repository_dependencies.xml Tue Feb 04 13:46:24 2014 -0500 +++ b/repository_dependencies.xml Thu Apr 03 11:02:03 2014 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> -<repositories description="These workflows require the deepTools repository."> - <repository changeset_revision="3fc7efe86cfc" name="deeptools" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repositories description="These workflows requires the deepTools repository."> + <repository changeset_revision="7d6d2f91843e" name="deeptools" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>