write_drake_params.Rd
write default values to drake_params.tsv for phipmake pipeline
write_drake_params(dir, screen_name, counts_filename = "counts.csv", counts_type = "Counts", enrichment_filename = "enrichment.csv", enrichment_type = "Enrichment", enrichment_threshold = 5, metadata_path = "/data/hlarman1/PhIPdb/Metadata/PeptideLibraries", output_extension = ".tsv")
dir | PhIP-seq project directory. |
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screen_name | Identifier for multiplexed screen, e.g. phipseq_0001. |
counts_filename | Name of demultiplexed, merged reads file in screen directory. |
counts_type | Identifier for type of counts data to append in output file names. |
enrichment_filename | Name of demultiplexed, merged enrichment file in screen directory. |
enrichment_type | Identifier for type of enrichment data to append in output file names. |
enrichment_threshold | Threshold enrichment value for determining hits. |
metadata_path | Directory path string to metadata folder containing peptide files and intrapeptide blast alignment files. |
output_extension | Extension for tab-separated output files. |