xslt works rather better if you have structured input rather than a fixed
set of flat variables. If you had a parameter show that took a list of
elements say <Replicates/><Metadata/>  then you could just do
<xsl:for-each select="$show">
 <xsl:if test="position()!=1">, </xsl:if>
 <xsl:apply-templates select="."/>
</xsl:for-each>

where templates matching Replicates would do whatever your pseudo code
Output("Reps") does.