app: inputs_metfrag: Predefine metfrag inputs.

* inputs_metfrag: New file.

DESCRIPTION

@@ -46,6 +46,7 @@ Roxygen: list(markdown = TRUE)
 Collate:
     'base.R'
     'resources.R'
+    'inputs_metfrag.R'
     'errors.R'
     'mix.R'
     'envopts.R'

R/inputs_metfrag.R

+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"]])