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copied!<p>Change from <code><xsl:template></code> to <code><xsl:apply-templates></code></p> <pre><code><xsl:apply-templates select="/data/peptides/peptide[generate-id()=generate-id(key('byAccSeq', concat(protein_accessions/accession, '|', sequence))[1])]" mode="type1" /> <xsl:apply-templates select="/data/peptides/peptide[generate-id()=generate-id(key('byAccSeq', concat(protein_accessions/accession, '|', sequence)))]" mode="type2" /> </code></pre> <p>After that, write <code><xsl:template></code> for both or in one accordingly.</p> <h1>Modify your solution in shorter way:</h1> <pre><code><xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> <xsl:output method="xml" indent="yes" omit-xml-declaration="yes"/> <xsl:key name="byAccSeq" match="/data/peptides/peptide" use="concat(accession, '|', sequence)"/> <xsl:param name="analysis" select="2"/> <xsl:template match="/"> <root> <name> <xsl:value-of select="$analysis"/> </name> <xsl:apply-templates select="data[peptides/peptide/accession=proteins/protein/accession]/peptides" /> </root> </xsl:template> <xsl:template match="peptides"> <xsl:choose> <xsl:when test="$analysis=1"> <xsl:copy-of select="peptide"/> </xsl:when> <xsl:otherwise> <xsl:for-each select="peptide[generate-id()=generate-id(key('byAccSeq', concat(accession, '|', sequence)))]"> <xsl:copy-of select="."/> </xsl:for-each> </xsl:otherwise> </xsl:choose> </xsl:template> </xsl:stylesheet> </code></pre> <p>I have tested my code as per your input XML & output. Now I can replicate the same.</p> <p>On my code, still I can reduce some more lines of code</p> <p>Replace <code><xsl:for-each></code> with below line:-</p> <pre><code><xsl:copy-of select="peptide[generate-id()=generate-id(key('byAccSeq', concat(accession, '|', sequence)))]"/> </code></pre> <p>Check it out..</p>

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