Better document SIRIUS summaries generation (#115)

taxonomicallyinformedannotation · Jan 16, 2024 · a45445c · a45445c
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diff --git a/NEWS.md b/NEWS.md
@@ -9,6 +9,7 @@
 * HMDB structures support
 * Optimize grep/gsub by adding `perl=TRUE` or `fixed=TRUE`
 * Update to Massbank version `2023.11`
+* Update SIRIUS preparation (#74, #115)
 
 # timaR 2.9.0
 

diff --git a/codemeta.json b/codemeta.json
@@ -513,7 +513,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "2851.826KB",
+  "fileSize": "2850.035KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -63,6 +63,7 @@ fbmn
 github
 gnps
 gsub
+gui
 https
 ilico
 inbo

diff --git a/vignettes/II-preparing.Rmd b/vignettes/II-preparing.Rmd
@@ -134,7 +134,8 @@ W
 ```
 
 These parameters were not optimized and were only used to give an example output.
-You can get the example running:
+If you are using the cli, do not forget the `W` to generate the summaries, or if you use the gui, generate them by clicking the corresponding icon.
+You can get an example running:
 
 ```{r get-sirius, results="hide", message=FALSE, warning=FALSE}
 source(file = "inst/scripts/get_example_sirius.R")
-Original file line number
+Diff line change
@@ Expand Up / @@ -63,6 +63,7 @@ fbmn @@
     github
     gnps
     gsub
+    gui
     https
     ilico
     inbo
@@ Expand Down @@