Workflow: wf_input_norm_and_entropy.cwl
Fetched 2024-04-26 04:01:43 GMT
Verified with cwltool version 3.1.20221201130942
This workflow normalizes clip aligned reads against a size-matched input sample. Then, an entropy score is calculated for each peak found.
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- Default Values
- Nested Workflows
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| peak_file | File | ||
| clip_bam_file | File | ||
| input_bam_file | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| input_norm |
overlap_peakfi_with_bam.cwl
(CommandLineTool)
|
This tool wraps overlap_peakfi_with_bam_PE.pl Usage: |
|
| compress_peaks |
compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat_outputfull.cwl
(CommandLineTool)
|
This tool wraps compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat_outputfull.pl, which merges neighboring or overlapping regions in a BED file. Usage: perl compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl <in.bed> <out.compressed.bed> |
|
| calculate_clip_readnum |
calculate_readnum.cwl
(CommandLineTool)
|
returns the number of reads inside a *.readnum file |
|
| calculate_input_readnum |
calculate_readnum.cwl
(CommandLineTool)
|
returns the number of reads inside a *.readnum file |
|
| create_entropybed_from_entropyfull |
full_to_bed.cwl
(CommandLineTool)
|
Converts a full file into a bed6 formatted file. |
|
| make_informationcontent_from_peaks |
make_informationcontent_from_peaks.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| entropy_bed | File | ||
| entropy_full | File | ||
| clip_read_num | File | ||
| compressed_bed | File | ||
| input_read_num | File | ||
| compressed_full | File | ||
| input_normed_bed | File | ||
| input_normed_full | File | ||
| entropy_excess_reads | File |
Permalink:
https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_input_norm_and_entropy.cwl
