Transform Biosample XML to TSV.

biosample2tsv.xsl

<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output omit-xml-declaration="yes" />
<!-- 
     Transform biosample XML to TSV.
     
     Usage: xsltproc biosample2tsv.xsl input.xml > output.tsv
-->
<xsl:template match="/">GEO<xsl:text>&#x9;</xsl:text>Title<xsl:text>&#x9;</xsl:text>CellLine<xsl:text>&#x9;</xsl:text>CellType<xsl:text>&#x9;</xsl:text>CdnaMethod<xsl:text>&#10;</xsl:text>
    <xsl:for-each select="//BioSample">
        <!-- GEO Id -->
        <xsl:value-of select="//Id[@db='GEO']" />
        <xsl:text>&#x9;</xsl:text>
        <!-- Title -->
        <xsl:if test="//Description/Title">
            <xsl:value-of select="//Description/Title" />
        </xsl:if>
        <xsl:text>&#x9;</xsl:text>
        <!-- Tab character
        <xsl:text>&#x9;</xsl:text>
        -->
        <!-- Cell Line -->
        <xsl:choose>
            <xsl:when test="//Attribute[@attribute_name='cell line']">
                <xsl:value-of select="//Attribute[@attribute_name='cell line']" />
            </xsl:when>
            <xsl:otherwise>NA</xsl:otherwise>
        </xsl:choose>
        <xsl:text>&#x9;</xsl:text>
        <!-- Cell Type -->
        <xsl:choose>
            <xsl:when test="//Attribute[@attribute_name='cell type']">
                <xsl:value-of select="//Attribute[@attribute_name='cell type']" />
            </xsl:when>
            <xsl:otherwise>NA</xsl:otherwise>
        </xsl:choose>
        <xsl:text>&#x9;</xsl:text>
        <!-- CDNA Method -->
        <xsl:choose>
            <xsl:when test="//Attribute[@attribute_name='cdna synthesis method']">
                <xsl:value-of select="//Attribute[@attribute_name='cdna synthesis method']" />
            </xsl:when>
            <xsl:otherwise>NA</xsl:otherwise>
        </xsl:choose>
        <!-- New line -->
        <xsl:text>&#10;</xsl:text>
    </xsl:for-each>
</xsl:template>
</xsl:stylesheet>