Workflow: Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses
Fetched 2023-01-09 19:35:23 GMT
Verified with cwltool version 3.1.20221201130942
Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| alias | String | Experiment short name/Alias | |
| header | Boolean (Optional) | Include header line |
Print header line in the output file |
| columns | String[] (Optional) | Columns to print |
List of columns to print (SELECT parameters for SQL query). Need to have format [chrom start end name]. No header. 4th columns should be unique, so we use a combination of chrom-start-end. |
| sql_query | String | Filtering parameters |
Filtering parameters (WHERE parameters for SQL query) |
| feature_file | File [TSV] | ChIP/ATAC experiment |
Called peaks file in TSV format with the nearest genes assigned |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| feature_select |
../tools/feature-select-sql.cwl
(CommandLineTool)
|
Feature select - filters TSV/CSV files based on the provided SQL query parameters |
Tool filters input TSV/CSV file based on the provided SQL query. Value set in sql_query parameter will be appended to the \"SELECT * FROM raw_data WHERE\". Column names in sql_query are case insensitive. Format of the input files is identified based on file extension *.csv - CSV *.tsv - TSV Otherwise used CSV by default. Output is always saved in TSV format. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_file | File [BED] | Filtered called peaks with the nearest genes assigned |
Regions of interest formatted as headerless BED file with [chrom start end name] |
| filtering_stderr_log | File [Textual format] | Filtering stderr log |
Filtering stderr log |
| filtering_stdout_log | File [Textual format] | Filtering stdout log |
Filtering stdout log |
https://w3id.org/cwl/view/git/f3e44d3b0f198cf5245c49011124dc3b6c2b06fd/workflows/filter-peaks-for-heatmap.cwl
