Mercurial > repos > iuc > ribowaltz_process

comparison ribowaltz.R @ 1:042cab870a39 draft default tip

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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
comparison
equal deleted inserted replaced
0:6d4c94373bba 1:042cab870a39
19 "gtffile", "g", 1, "character", 19 "gtffile", "g", 1, "character",
20 "codon_coverage_info", "Y", 1, "character", 20 "codon_coverage_info", "Y", 1, "character",
21 "cds_coverage_info", "Z", 1, "character", 21 "cds_coverage_info", "Z", 1, "character",
22 "psite_info_rdata", "O", 0, "character", 22 "psite_info_rdata", "O", 0, "character",
23 "refseq_sep", "s", 0, "character", 23 "refseq_sep", "s", 0, "character",
24 "indel_threshold", "t", 0, "integer",
24 "params_duplicate_filterting", "d", 0, "character", 25 "params_duplicate_filterting", "d", 0, "character",
25 "params_peridiocity_filterting", "l", 0, "character", 26 "params_peridiocity_filterting", "l", 0, "character",
26 "params_custom_filterting", "c", 0, "character", 27 "params_custom_filterting", "c", 0, "character",
27 "params_psite_additional", "p", 0, "character", 28 "params_psite_additional", "p", 0, "character",
28 "params_coverage_additional", "C", 0, "character" 29 "params_coverage_additional", "C", 0, "character"
46 sep <- opt$refseq_sep 47 sep <- opt$refseq_sep
47 if (opt$refseq_sep == "") { 48 if (opt$refseq_sep == "") {
48 sep <- NULL 49 sep <- NULL
49 } 50 }
50 # convert alignments in BAM files into list of data tables 51 # convert alignments in BAM files into list of data tables
51 reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep) 52 reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep, indel_threshold = opt$indel_threshold)
52 53
53 library("jsonlite") 54 library("jsonlite")
54 # remove duplicate reads 55 # remove duplicate reads
55 if (!is.null(opt$params_duplicate_filterting)) { 56 if (!is.null(opt$params_duplicate_filterting)) {
56 json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting) 57 json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting)
61 ) 62 )
62 } 63 }
63 64
64 # selection of read lengths - periodicity filtering 65 # selection of read lengths - periodicity filtering
65 if (!is.null(opt$params_peridiocity_filterting)) { 66 if (!is.null(opt$params_peridiocity_filterting)) {
66 json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting) 67 json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
67 reads_list <- length_filter( 68 reads_list <- length_filter(
68 data = reads_list, 69 data = reads_list,
69 length_filter_mode = "periodicity", 70 length_filter_mode = "periodicity",
70 periodicity_threshold = json_peridiocity_filterting$periodicity_threshold 71 periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
71 ) 72 )
72 } 73 }
73 # selection of read lengths - length range filtering 74 # selection of read lengths - length range filtering
74 if (!is.null(opt$params_custom_filterting)) { 75 if (!is.null(opt$params_custom_filterting)) {
75 json_custom_filterting <- fromJSON(opt$params_custom_filterting) 76 json_custom_filterting <- fromJSON(opt$params_custom_filterting)
76 reads_list <- length_filter( 77 reads_list <- length_filter(
77 data = reads_list, 78 data = reads_list,
78 length_filter_mode = "custom", 79 length_filter_mode = "custom",
79 length_range = json_custom_filterting$length_range 80 length_range = json_custom_filterting$length_range
80 ) 81 )
81 } 82 }
82 83
83 # compute P-site offset 84 # compute P-site offset
84 json_psite_additional <- fromJSON(opt$params_psite_additional) 85 json_psite_additional <- fromJSON(opt$params_psite_additional)
85 psite_offset <- psite( 86 psite_offset <- psite(