Workflow: analysis.cwl

Fetched 2019-12-07 04:17:15 GMT
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Inputs

ID Type Title Doc
input_mirna File
output_file_name String
input_mrna File
settings_contextLen_L Integer
input_multiple_alignments File
input_coords File[]
settings_split_by String
input_tree File
settings_mirza_threshold Float
settings_contextLen_U Integer
input_model_with_bls File
settings_index_after_split Integer
input_model_without_bls File

Steps

ID Runs Label Doc
concatenate_results
concatenate.cwl (CommandLineTool)
calculate_contrafold
calculate_contrafold.cwl (CommandLineTool)

The `CONTRAfold <http://contra.stanford.edu/contrafold/>`_ algorithm is used to calculate accessibility of target site for miRNA.

merge_results_add_probability_and_calculate_per_gene_score
merge_results_add_probability_and_calculate_per_gene_score.cwl (CommandLineTool)

Merge all results into one features table

calculate_flanks
calculate_flanks_composition.cwl (CommandLineTool)

Calculate flanks composition using provided coordinates.

calculate_mirza
calculate_MIRZA.cwl (CommandLineTool)

Calculate MIRZA interaction energy and MIRZA-based Branch Length Score (conservation) for the provided coordinates of putative targets.

calculate_distance
calculate_distance.cwl (CommandLineTool)

Calculate distance to the boundary based on provided coordinates for targets.

Outputs

ID Type Label Doc
output File
Permalink: https://w3id.org/cwl/view/git/b4a38d00a8d6e27540217ac5d590ab8a5da0a92e/tools/analysis.cwl