bioinformatics: use subject_section in header (#415)

* use subject_section in header fixes #414 * separate manuscript_type and subject_section #414 #415 * update NEWS.md to mention manuscript_type and subject_section in template and skeleton * avoids breaking change by making manuscript_type fallback to subject_section as default if not entered Co-authored-by: Christophe Dervieux <christophe.dervieux@gmail.com>
rstudio · Jun 29, 2021 · 1d26f7d · 1d26f7d
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diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,7 @@ rticles 0.21
 ---------------------------------------------------------------------
 
 - `bioinformatics_article()` has no more trailing comma after last author (thanks, @stephenturner, #413).
+- `bioinformatics_article()` now separates `manuscript_type` (e.g., Applications note, Original article) and `subject_section` (e.g. Genome analysis, Phylogenetics) in template and skeleton (thanks, @stephenturner, #415)
 
 rticles 0.20
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diff --git a/inst/rmarkdown/templates/bioinformatics/resources/template.tex b/inst/rmarkdown/templates/bioinformatics/resources/template.tex
@@ -49,7 +49,7 @@
 % \usepackage[colorlinks=true, allcolors=blue]{hyperref}
 
 \access{Advance Access Publication Date: $access_date.day$ $access_date.month$ $access_date.year$}
-\appnotes{Manuscript Category}
+\appnotes{$if(manuscript_type)$$manuscript_type$$else$$subject_section$$endif$}
 
 \begin{document}
 \firstpage{1}

diff --git a/inst/rmarkdown/templates/bioinformatics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/bioinformatics/skeleton/skeleton.Rmd
@@ -2,8 +2,22 @@
 title_full: Template for preparing a submission to Bioinformatics using RMarkdown
 title_short: Bioinformatics Rmd Template
 
-# one of `Original Paper`, `Discovery Note`, `Application Note`, `Review`, `Letter to the Editor`, `Conference Paper`    
-subject_section: Application Note
+# One of the following below. See https://academic.oup.com/bioinformatics/pages/instructions_for_authors#Types%20of%20Manuscript
+# one of `Original Paper`, `Discovery Note`, `Applications Note`, `Review`, `Letter to the Editor`, `Conference Paper`    
+manuscript_type: Application Note
+
+# One of the following below. See https://academic.oup.com/bioinformatics/pages/instructions_for_authors#Detailed%20Scope%20Guidelines
+# Genome analysis
+# Sequence analysis
+# Phylogenetics
+# Structural bioinformatics
+# Gene expression
+# Genetic and population analysis
+# Systems biology
+# Data and text mining
+# Databases and ontologies
+# Bioimage informatics
+subject_section:  Genome analysis
 
 access_date:
   - day: DD