my $SIPHTseq_PTU_parse = newTransformation (NS, 'SIPHTseq_PTU_parse', '1.0');

$SIPHTseq_PTU_parse -> uses (newFilename (name => 'PTU_homol_add.sh', %exec));
$SIPHTseq_PTU_parse -> uses (newFilename (name => 'PTU_para_add.sh', %exec));
$SIPHTseq_PTU_parse -> uses (newFilename (name => 'PTU_TFBS_add.sh', %exec));

$adag -> addTransformation ($SIPHTseq_PTU_parse);

Generates output as

<executable namespace="sipht" name="SIPHTseq_PTU_parse" version="1.0">
<uses name="PTU_para_add.sh" />
<uses name="PTU_homol_add.sh" />
<uses name="PTU_TFBS_add.sh" />
</executable>

executable should be replaced with transformation.