From a86ef4eda927c47791dc0c25852c13ea622f809b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 11:43:19 +1100
Subject: draft API docs for BWA and strelka

---
 doc/tools-doc.nix | 41 +++++++++++++++++++++++++++++++++++++++++
 doc/tools.xml     | 14 ++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 doc/tools-doc.nix
 create mode 100644 doc/tools.xml

(limited to 'doc')

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>
-- 
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