From ceae362068ed73dc2a3ea26a1be302420f53ffdc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Tue, 10 Jan 2023 01:10:04 +0100
Subject: [PATCH] app, resources: Add MetFrag config pane.
---
DESCRIPTION | 2 +-
R/resources.R | 15 +++++++++++++++
inst/rmd/app.Rmd | 43 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 59 insertions(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index a12d71b..f33b90a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
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:
diff --git a/R/resources.R b/R/resources.R
index b4823f7..98b115a 100644
--- a/R/resources.R
+++ b/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")
+
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index a0a04ac..c557b26 100644
--- a/inst/rmd/app.Rmd
+++ b/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>
--
GitLab