Add parameters to the documentation

Author: alchemistmatt

docs/MSGFPlus.html

@@ -89,6 +89,10 @@ <h1>MS-GF+</h1>
 
 <span class="code-keyword">[-maxMissedCleavages Count]</span> (Exclude peptides with more than this number of missed cleavages from the search; <span class="code-object">Default: -1 (no limit)</span>)
 
+<span class="code-keyword">[-minNumPeaks Count]</span> (Minimum number of ions a spectrum must have to be examined; <span class="code-object">Default: 10</span>)
+
+<span class="code-keyword">[-iso NumIsoforms]</span> (Number of isoforms to consider per peptide; <span class="code-object">Default: 128</span>)
+
 <span class="code-keyword">[-numMods Count]</span> (Maximum number of dynamic (variable) modifications per peptide; <span class="code-object">Default: 3</span>)
 
 <span class="code-keyword">[-allowDenseCentroidedPeaks 0/1]</span> (<span class="code-object">Default: 0 (disabled)</span>; 1: (for mzML/mzXML input only) allows inclusion of spectra with high-density centroid data in the search)