sign.js

var SignedXml = require('xml-crypto').SignedXml
  , fs = require('fs')

var xml = `<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"><soap:Header><certificateNumber xmlns="https://allpay.kz">27</certificateNumber></soap:Header><soap:Body><ns2:createCashInTransaction xmlns:ns2="http://www.allpay.kz/mfs/soap/TransactionManagement/1.1"><CashInRequest><header><lang>ru</lang><timestamp>2018-08-10T19:04:11.385+06:00</timestamp><requester>10124213</requester></header><toUserName>77072734954</toUserName><amount>10</amount><GUID>fa495ffa-4825-485e-9b14-a04c6d8315d2</GUID></CashInRequest></ns2:createCashInTransaction></soap:Body></soap:Envelope>`

var sig = new SignedXml(null)
sig.signatureAlgorithm = "http://www.w3.org/2000/09/xmldsig#rsa-sha1"
sig.canonicalizationAlgorithm = "http://www.w3.org/2001/10/xml-exc-c14n#WithComments"

sig.addReference(
  // reference to the root node
  "/*",
  [
    'http://www.w3.org/2000/09/xmldsig#enveloped-signature'
  ],
  'http://www.w3.org/2000/09/xmldsig#sha1',
  '',
  '',
  '',
  // let the URI attribute with an empty value,
  // this is the signal that the signature is affecting the whole xml document
  true
);

sig.signingKey = fs.readFileSync("client.pem")
sig.computeSignature(xml)
fs.writeFileSync("signed.xml", sig.getSignedXml())