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-rw-r--r--doc/tools-doc.nix41
-rw-r--r--doc/tools.xml14
2 files changed, 55 insertions, 0 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
new file mode 100644
index 0000000..b2cd7ba
--- /dev/null
+++ b/doc/tools-doc.nix
@@ -0,0 +1,41 @@
+{ bionix ? import ./.. {} }:
+
+with bionix;
+
+stage {
+ name = "tools-docs";
+ src = ../tools;
+
+ xsltFlags = lib.concatStringsSep " " [
+ #"--param section.autolabel 1"
+ #"--param section.label.includes.component.label 1"
+ #"--stringparam html.stylesheet 'style.css overrides.css highlightjs/mono-blue.css'"
+ #"--stringparam html.script './highlightjs/highlight.pack.js ./highlightjs/loader.js'"
+ #"--param xref.with.number.and.title 1"
+ #"--param toc.section.depth 3"
+ #"--stringparam admon.style ''"
+ #"--stringparam callout.graphics.extension .svg"
+ ];
+
+
+ buildInputs = with pkgs; [ nixdoc libxslt libxml2 ];
+ installPhase = ''
+ function docgen {
+ nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml"
+ }
+
+ docgen bwa 'BWA aligner'
+ docgen strelka 'Strelka2 variant caller'
+
+ mkdir $out
+ cp ${./tools.xml} tools.xml
+ xmllint --nonet --xinclude --noxincludenode tools.xml --output tools-full.xml
+ cat tools-full.xml
+ xsltproc $xsltFlags \
+ --nonet \
+ --xinclude \
+ --output $out/index.html \
+ ${pkgs.docbook_xsl_ns}/xml/xsl/docbook/epub/docbook.xsl \
+ tools-full.xml
+ '';
+}
diff --git a/doc/tools.xml b/doc/tools.xml
new file mode 100644
index 0000000..f23dfeb
--- /dev/null
+++ b/doc/tools.xml
@@ -0,0 +1,14 @@
+<book xmlns="http://docbook.org/ns/docbook"
+ xmlns:xi="http://www.w3.org/2001/XInclude">
+ <info>
+ <title>Bionix</title>
+ </info>
+ <section xmlns="http://docbook.org/ns/docbook"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:xi="http://www.w3.org/2001/XInclude"
+ xml:id="sec-tools">
+ <title>Tools</title>
+ <xi:include href="bwa.xml" />
+ <xi:include href="strelka.xml" />
+ </section>
+</book>