- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
input_mrna | File | ||
input_tree | File | ||
input_mirna | File | ||
output_file_name | String | ||
settings_split_by | String | ||
input_model_with_bls | File | ||
settings_contextLen_L | Integer | ||
settings_contextLen_U | Integer | ||
input_model_without_bls | File | ||
settings_mirza_threshold | Float | ||
input_multiple_alignments | File | ||
settings_index_after_split | Integer |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
mirza |
tools/mirza.cwl
(CommandLineTool)
|
||
split |
tools/split_mirza_results.cwl
(CommandLineTool)
|
||
analyze |
tools/analysis.cwl
(Workflow)
|
||
mirza_parser |
tools/extract_data_from_mirza_output.cwl
(CommandLineTool)
|
Take MIRZA output and arrange it in a proper way |
|
prepare_mirnas |
tools/prepare_mirnas.cwl
(CommandLineTool)
|
Prepare miRNA fasta file for MIRZA i.e. for each miRNA sequence check if it is 21 nucleotide long and if not eliminate it. It also replaces all u or U into T. In the same time it splits miRNAs into separate files. |
|
concatenate_mirza |
tools/concatenate.cwl
(CommandLineTool)
|
||
mirna_expressions |
tools/generate_mirna_expressions.cwl
(CommandLineTool)
|
||
generate_mrna_chunks |
tools/generate_mrna_chunks.cwl
(CommandLineTool)
|
Take mRNAs and generate fragments by sliding window that can be fed into MIRZA |
|
filter_duplicates_from_scan |
tools/filter_duplicates_from_scan.cwl
(CommandLineTool)
|
Filter duplicates in coordinates by id, miRNA and sequence |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
mirzag_output | File |
Permalink:
https://w3id.org/cwl/view/git/b4a38d00a8d6e27540217ac5d590ab8a5da0a92e/mirzag_scan.cwl