Merge GS-Amat support to development#153
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madc2vcf updates
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| choices = list("Target"= "target", "Target + Off-Target" = "target_off", "Microhaplotypes" = "multiallelic"), | ||
| selected = "target"), | ||
| selectInput(ns('species'), | ||
| label = 'Species', | ||
| choices = c("alfalfa","blueberry", "cranberry", "cucumber", "lettuce", "pecan", "sweetpotato", "other"), | ||
| choices = c("alfalfa", "blueberry", "cranberry", "cucumber", "pecan", "potato", "strawberry", "sweetpotato", "other"), | ||
| selected = "alfalfa"), | ||
| conditionalPanel(condition = "input.snp_type == 'target_off'", | ||
| ns = ns, | ||
| conditionalPanel(condition = "input.species == 'other'", | ||
| ns = ns, | ||
| fileInput(ns("botloci_file"), "Upload bottom strand probes file (.botloci)"), | ||
| fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"), | ||
| fileInput(ns("markers_info_file"), "Upload markers information (_lut.csv from HapApp) (optional)"), | ||
| ), | ||
| fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"), | ||
| sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1) | ||
| sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = max(1, availableCores() - 1), value = 1, step = 1), br(), | ||
| div( | ||
| style = "text-align: left; margin-top: 10px;", | ||
| actionButton(ns("advanced_options_all"), | ||
| label = HTML(paste(icon("cog", style = "color: #007bff;"), "Advanced Options")), | ||
| style = "background-color: transparent; border: none; color: #007bff; font-size: smaller; text-decoration: underline; padding: 0;" | ||
| ) | ||
| ) | ||
| ), | ||
| conditionalPanel(condition = "input.snp_type == 'target'", | ||
| ns = ns, | ||
| radioButtons(ns("collapse_matches_counts"), | ||
| label = "Collapse Matches Counts:", | ||
| choices = list("Yes"= TRUE, "No" = FALSE), | ||
| selected = FALSE), | ||
| conditionalPanel(condition = "input.species == 'other'", | ||
| ns = ns, | ||
| radioButtons(ns("ref_alt"), | ||
| label = "Extract REF and ALT info:", | ||
| choices = list("Yes"= "TRUE", "No" = "FALSE"), | ||
| selected = "TRUE"), | ||
| choices = list("Yes"= TRUE, "No" = FALSE), | ||
| selected = TRUE), | ||
| conditionalPanel(condition = "input.ref_alt == 'TRUE'", | ||
| ns = ns, | ||
| fileInput(ns("botloci_file"), "Upload bottom strand probes file (.botloci)"), | ||
| fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"), | ||
| fileInput(ns("markers_info_file"), "Upload markers information (_lut.csv from HapApp) (optional)"), | ||
| ) | ||
| ) | ||
| ) |
| verbose = TRUE) | ||
| } else if(input$snp_type == "target"){ | ||
| madc2vcf_targets(read_madc, output_name, get_REF_ALT = as.logical(input$ref_alt), botloci_file = botloci, | ||
| markers_info = markers_info, collapse_matches_counts = input$collapse_matches_counts) |
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| madc2vcf_multi( | ||
| madc_file = read_madc, | ||
| botloci_file = botloci, | ||
| outfile = output_name, | ||
| markers_info = markers_info, | ||
| ploidy = 4L, |
| @@ -268,106 +431,101 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){ | |||
| showCancelButton = FALSE, | |||
| animation = TRUE | |||
| ) | |||
|
|
||
| error_if_true <- c( | ||
| "multiallelics", "phased_GT", "mixed_ploidies", |
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| radioButtons(ns("ref_alt"), | ||
| label = "Extract REF and ALT info:", | ||
| choices = list("Yes"= "TRUE", "No" = "FALSE"), | ||
| selected = "TRUE"), | ||
| choices = list("Yes"= TRUE, "No" = FALSE), | ||
| selected = TRUE), | ||
| conditionalPanel(condition = "input.ref_alt == 'TRUE'", | ||
| ns = ns, | ||
| fileInput(ns("botloci_file"), "Upload bottom strand probes file (.botloci)"), | ||
| fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"), | ||
| fileInput(ns("markers_info_file"), "Upload markers information (_lut.csv from HapApp) (optional)"), | ||
| ) |
alex-sandercock
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May 17, 2026
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existing changes from previous branch review
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|
Re-run the checks after BIGr v0.7.2 is finished being available on CRAN for ubuntu distros |
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