{ 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 ascat 'ascatNGS CNV caller'
    docgen bowtie 'Bowtie aligner'
    docgen bwa 'BWA aligner'
    docgen cnvkit 'CNVkit CNV caller'
    docgen facets 'Facets CNV caller'
    docgen fastqc 'FastQC quality control'
    docgen gridss 'GRIDSS SV caller'
    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
  '';
}