diff --git a/DESCRIPTION b/DESCRIPTION index 2059e218fa0a573e8628f19ce678fa49819add65..6f0ba6cb2ad985b59b0824b268bb9b488bcb3c46 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -46,6 +46,7 @@ Roxygen: list(markdown = TRUE) Collate: 'base.R' 'resources.R' + 'inputs_metfrag.R' 'errors.R' 'mix.R' 'envopts.R' diff --git a/R/inputs_metfrag.R b/R/inputs_metfrag.R new file mode 100644 index 0000000000000000000000000000000000000000..4d840511fec142ecf3fccb4bf443dd15fc8a8d0d --- /dev/null +++ b/R/inputs_metfrag.R @@ -0,0 +1,77 @@ +mk_shiny_control <- function(name,fun,args) { + content = do.call(what=fun,args=c(list(inputId=name),args)) + res = list(name=name, + fun=fun, + content=content) + res +} + +INPUTS_METFRAG_NUMERIC = list(mk_shiny_control(name="mf_database_search_relative_mass_deviation", + fun="numericInput", + args=list(label="Database search relative mass deviation", + value=5)), + mk_shiny_control(name="mf_fragment_peak_match_absolute_mass_deviation", + fun="numericInput", + args=list(label="Fragment peak match absolute mass deviation", + value=METFRAG_DEFAULT_ABSMASSDEV)), + mk_shiny_control(name="mf_fragment_peak_match_relative_mass_deviation", + fun="numericInput", + args=list(label="Fragment peak match relative mass deviation", + value=METFRAG_DEFAULT_RELMASSDEV)), + mk_shiny_control(name="mf_maximum_tree_depth", + fun="numericInput", + args=list(label="MaximumTreeDepth", + value=METFRAG_DEFAULT_MAX_TREE_DEPTH))) + +INPUTS_METFRAG_SELECT = list(mk_shiny_control(name="mf_pre_processing_candidate_filter", + fun="selectInput", + args=list(label="Preprocessing candidate filter", + choices=shinyscreen:::METFRAG_PREPFLT_CHOICES, + selected=shinyscreen:::METFRAG_PREPFLT_DEFAULT, + multiple=T)), + mk_shiny_control(name="mf_post_processing_candidate_filter", + fun="selectInput", + args=list(label="Postprocessing candidate filter", + choices=shinyscreen:::METFRAG_POSTPFLT_CHOICES, + selected=shinyscreen:::METFRAG_POSTPFLT_DEFAULT, + multiple=T)), + mk_shiny_control(name="mf_metfrag_candidate_writer", + fun="selectInput", + args=list(label="MetFrag Candidate Writer", + choices=shinyscreen:::METFRAG_WRITER_CHOICES, + selected=shinyscreen:::METFRAG_DEFAULT_WRITER)), + mk_shiny_control(name="mf_database_type", + fun="selectInput", + args=list(label="Database type", + choices=METFRAG_DATABASE_TYPE, + selected=METFRAG_DEFAULT_DATABASE_TYPE)), + mk_shiny_control(name="mf_local_database", + fun="selectInput", + args=list(label="Local Database", + choices=character(0))), + mk_shiny_control(name="mf_local_db_col_ident", + fun="selectInput", + args=list(label="Select Identifiers", + multiple = T, + choices=character(0))), + mk_shiny_control(name="mf_local_db_col_coll", + fun="selectInput", + args=list(label="Identifiers for sets of results", + multiple = T, + choices=character(0))), + mk_shiny_control(name="mf_scores_intrinsic", + fun="selectInput", + args=list(label="Select Scoring Types", + choices = METFRAG_INTRINSIC_SCORES, + multiple = T, + selected = names(METFRAG_DEFAULT_SCORES))), + mk_shiny_control(name="mf_local_db_col_scores", + fun="selectInput", + args=list(label="Select local scoring terms", + multiple = T, + choices=character(0)))) + + +INPUTS_METFRAG = c(INPUTS_METFRAG_NUMERIC, INPUTS_METFRAG_SELECT) + +names(INPUTS_METFRAG) = sapply(INPUTS_METFRAG, function(x) x[["name"]])