Mercurial > repos > iuc > ribowaltz_process
diff ribowaltz.R @ 1:042cab870a39 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
| author | iuc |
|---|---|
| date | Mon, 23 Oct 2023 12:10:31 +0000 |
| parents | 6d4c94373bba |
| children |
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--- a/ribowaltz.R Thu Sep 22 20:30:54 2022 +0000 +++ b/ribowaltz.R Mon Oct 23 12:10:31 2023 +0000 @@ -21,6 +21,7 @@ "cds_coverage_info", "Z", 1, "character", "psite_info_rdata", "O", 0, "character", "refseq_sep", "s", 0, "character", + "indel_threshold", "t", 0, "integer", "params_duplicate_filterting", "d", 0, "character", "params_peridiocity_filterting", "l", 0, "character", "params_custom_filterting", "c", 0, "character", @@ -48,7 +49,7 @@ sep <- NULL } # convert alignments in BAM files into list of data tables -reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep) +reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep, indel_threshold = opt$indel_threshold) library("jsonlite") # remove duplicate reads @@ -63,21 +64,21 @@ # selection of read lengths - periodicity filtering if (!is.null(opt$params_peridiocity_filterting)) { - json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting) - reads_list <- length_filter( - data = reads_list, - length_filter_mode = "periodicity", - periodicity_threshold = json_peridiocity_filterting$periodicity_threshold - ) + json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting) + reads_list <- length_filter( + data = reads_list, + length_filter_mode = "periodicity", + periodicity_threshold = json_peridiocity_filterting$periodicity_threshold + ) } # selection of read lengths - length range filtering if (!is.null(opt$params_custom_filterting)) { - json_custom_filterting <- fromJSON(opt$params_custom_filterting) - reads_list <- length_filter( - data = reads_list, - length_filter_mode = "custom", - length_range = json_custom_filterting$length_range - ) + json_custom_filterting <- fromJSON(opt$params_custom_filterting) + reads_list <- length_filter( + data = reads_list, + length_filter_mode = "custom", + length_range = json_custom_filterting$length_range + ) } # compute P-site offset