From 1d26f7d2268cdeada165b54d6b9cdc0a1e3f8c65 Mon Sep 17 00:00:00 2001 From: Stephen Turner Date: Tue, 29 Jun 2021 14:01:20 -0400 Subject: [PATCH] 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 --- NEWS.md | 1 + .../bioinformatics/resources/template.tex | 2 +- .../bioinformatics/skeleton/skeleton.Rmd | 18 ++++++++++++++++-- 3 files changed, 18 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 778c80218..d97b4619b 100644 --- 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 --------------------------------------------------------------------- diff --git a/inst/rmarkdown/templates/bioinformatics/resources/template.tex b/inst/rmarkdown/templates/bioinformatics/resources/template.tex index 707964c7f..0b086cf13 100644 --- 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 index 8db103653..cbfe6b0aa 100644 --- 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