anchor.diff:  <!--   --><b>$</b> umgap-visualize.sh -i tryptic-sensitivity-output.fa.gz -w > tryptic-sensitivity.html
   <!--   --><b>$</b> umgap-visualize.sh -i tryptic-sensitivity-output.fa.gz -u
   <!--   --><a href="https://bl.ocks.org/11b7809d6754b9530cf1a49d93a8d568">https://bl.ocks.org/11b7809d6754b9530cf1a49d93a8d568</a></pre>
  +        <p>
  +          The CSV tables contain a record for each taxon found in the sample.
  +          A record contains, in order, the frequency of the taxon, the taxon ID and (for convenience) the taxon name.
  +          All records will be at the same specified taxon rank or at root (unidentified).
  +        </p>
  +        <dl class='dl-horizontal'>
  +          <dt><samp>-i file</samp></dt><dd>Analysis output file, optionally compressed.</dd>
  +          <dt><samp>-t</samp></dt><dd>Output a CSV frequency table on species rank.</dd>
  +          <dt><samp>-w</samp></dt><dd>Output an HTML webpage of an interactive visualization.</dd>
  +          <dt><samp>-u</samp></dt><dd>Print a shareable URL to a online interactive visualisation.</dd>
  +          <dt><samp>-r rank</samp></dt><dd>Set the rank for the CSV frequency table (default: species).</dd>
  +        </dl>
         </div>
  -      <dl class='dl-horizontal'>
  -        <dt><samp>-i file</samp></dt><dd>Analysis output file, optionally compressed.</dd>
  -        <dt><samp>-t</samp></dt><dd>Output a CSV frequency table on species rank.</dd>
  -        <dt><samp>-w</samp></dt><dd>Output an HTML webpage of an interactive visualization.</dd>
  -        <dt><samp>-u</samp></dt><dd>Print a shareable URL to a online interactive visualisation.</dd>
  -        <dt><samp>-r rank</samp></dt><dd>Set the rank for the CSV frequency table (default: species).</dd>
  -      </dl>
       </div>
   
       <h2>References</h2>
  
positive.code:       <div class="card-supporting-text">
          <p>
            When setup is complete, the analyse script will automatically use the downloaded databases and linked tools.
            Here we will run 2 preconfigured pipelines on the same input data.
            The input data consists of a 100 paired-end reads sampled from a dataset
              generated by Lindgreen <i>et al.</i> (2016) for their metabenchmark.
            With these paired-end reads in the <code>sample-1.fq</code> and <code>sample-2.fq</code> files,
              the command is as follows.
          </p>
          <pre style="max-height: initial;">
  <!--   --><b>$</b> umgap-analyse.sh -1 sample-1.fq -2 sample-2.fq -t tryptic-precision -o tryptic-precision-output.fa -1 sample-1.fq -2 sample-2.fq -t tryptic-sensitivity -z -o tryptic-sensitivity-output.fa.gz
  <!--   --><b>$</b> head -2 tryptic-precision-output.fa
  <!--   --><b>$</b> zcat tryptic-precision-output.fa.gz | head -2</pre>
          <dl class='dl-horizontal'>
            <dt><samp>-c dir</samp></dt><dd>Set a different configuration directory.</dd>
            <dt><samp>-z</samp></dt><dd>Request compression of the output file.</dd>
            <dt><samp>-1 file</samp></dt><dd>Single ended (or first pair-ended) FASTA or FASTQ input file, optionally compressed.</dd>
            <dt><samp>-2 file</samp></dt><dd>Second pair-ended FASTA or FASTQ input file, optionally compressed.</dd>
            <dt><samp>-t</samp></dt><dd>Type of the analysis (high precision by default).</dd>
            <dt><samp>-o file</samp></dt><dd>The output file.</dd>
          </dl>
  
negative.code:       <div class="card-supporting-text">
          <p>
            After analysis, you probably want to view the results.
            While the analyse script output format is easily parsed,
             you can also use the visualize script to create importable CSV frequency tables
             and interactive visualisations.
            The interactive visualisations can be stored locally or hosted online.
            The following snippet creates all three in turn.
          </p>
          <pre style="max-height: initial;">
  <!--   --><b>$</b> umgap-visualize.sh -i tryptic-precision-output.fa -t -r phylum
  <!--   -->2	1117	Cyanobacteria
  <!--   -->4	57723	Acidobacteria
  <!--   -->4	201174	Actinobacteria
  