app, resources: Add MetFrag config pane.

DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 1.2.5
+Version: 1.2.9000
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 

R/resources.R

@@ -309,3 +309,18 @@ PLOT_EIC_ASPECT <- 0.75
 ## possibility that each set connects to a different collection of
 ## files.
 COLRDATA_KEY <- "set"
+
+## METFRAG
+
+METFRAG_ADDUCTS = c("[M+H]+","[M+NH4]+","[M+Na]+","[M+K]+",
+                    "[M+CH3OH+H]+","[M+ACN+H]+","[M+ACN+Na]+","[M+2ACN+H]+",
+                    "[M-H]-","[M+Cl]-","[M+HCOO]-","[M+CH3COO]-","[M]+/-")
+METFRAG_WRITER_CHOICES = c("CSV","PSV","XLS")
+METFRAG_DEFAULT_WRITER = "CSV"
+METFRAG_DATABASE_TYPE = c("KEGG","PubChem","ExtendedPubChem","LocalSDF","LocalPSV","LocalCSV")
+METFRAG_DEFAULT_DATABASE_TYPE = "LocalCSV"
+METFRAG_PREPFLT_CHOICES = c("UnconnectedCompoundFilter","IsotopeFilter")
+METFRAG_PREPFLT_DEFAULT = c("UnconnectedCompoundFilter","IsotopeFilter")
+METFRAG_POSTPFLT_CHOICES = c("InChIKeyFilter")
+METFRAG_POSTPFLT_DEFAULT = c("InChIKeyFilter")
+

inst/rmd/app.Rmd

@@ -493,6 +493,49 @@ shinyscreen::rt_input(input_rt = "ret_time_shift_tol",
                       def_unit = vu[['unit']])
 ```
 
+### MetFrag (experimental, optional)
+
+If `java` and `MetFragCL` are available, Shinyscreen can run
+`MetFragCL`. The configuration is a subset of what a MetFrag config
+file looks like.
+
+```{r, echo=F}
+numericInput("mf_database_search_relative_mass_deviation",
+             label="Database search relative mass deviation",
+             value=5)
+numericInput("mf_fragment_peak_match_absolute_mass_deviation",
+             label="Fragment peak match absolute mass deviation",
+             value=5)
+numericInput("mf_fragment_peak_match_relative_mass_deviation",
+             label="Fragment peak match relative mass deviation",
+             value=5)
+numericInput("mf_maximum_tree_depth",
+             label="MaximumTreeDepth",
+             value=2)
+selectInput("mf_metfrag_candidate_writer",
+            label="MetFrag Candidate Writer",
+            choices=shinyscreen:::METFRAG_WRITER_CHOICES,
+            selected=shinyscreen:::METFRAG_DEFAULT_WRITER)
+selectInput("mf_database_type",
+            label="Database type",
+            choices=shinyscreen:::METFRAG_DATABASE_TYPE,
+            selected=shinyscreen:::METFRAG_DEFAULT_DATABASE_TYPE)
+selectInput("mf_local_database_path","Local Database Path",
+            choices=NA_character_,
+            selected=NA_character_)
+selectInput("mf_pre_processing_candidate_filter",
+            label="Preprocessing candidate filter",
+            choices=shinyscreen:::METFRAG_PREPFLT_CHOICES,
+            selected=shinyscreen:::METFRAG_PREPFLT_DEFAULT,
+            multiple=T)
+selectInput("mf_post_processing_candidate_filter",
+            label="Postprocessing candidate filter",
+            choices=shinyscreen:::METFRAG_POSTPFLT_CHOICES,
+            selected=shinyscreen:::METFRAG_POSTPFLT_DEFAULT,
+            multiple=T)
+textInput("mf_score_types",label="Score Types",value="FragmenterScore,AutomatedPeakFingerprintAnnotationScore,AutomatedLossFingerprintAnnotationScore,OfflineIndividualMoNAScore")
+textInput("mf_score_weights",label="Score Weights",value="1.,1.,1.,1.")
+```
 ### Report
 
 <details><summary>Create a report</summary>