I wrote PHP library for Coveralls. https://github.com/satooshi/php-coveralls PHP script for Coveralls. clover.xml generated by PHPUnit is required to get coverage data. And repo_token for Coveralls repository is required for API access.

coveralls.php

<?php

// data

/**
 * Data represents "source_files" element of Coveralls' "json_file".
 *
 * @author Kitamura Satoshi <[email protected]>
 */
class SourceFile
{
    /**
     * Source filename.
     *
     * @var string
     */
    protected $name;

    /**
     * Source content.
     *
     * @var string
     */
    protected $source;

    /**
     * Coverage data of the source file.
     *
     * @var array
     */
    protected $coverage;

    /**
     * Absolute path.
     *
     * @var string
     */
    protected $path;

    /**
     * Line number of the source file.
     *
     * @var integer
     */
    protected $fileLines;

    /**
     * Constructor.
     *
     * @param string $path Absolute path.
     * @param string $name Source filename.
     * @param string $eol  End of line.
     */
    public function __construct($path, $name, $eol = "\n")
    {
        $this->path   = $path;
        $this->name   = $name;
        $this->source = file_get_contents($path);

        $lines = explode($eol, $this->source);
        $this->fileLines = count($lines);
        $this->coverage = array_fill(0, $this->fileLines, null);
    }

    /**
     * String expression (convert to json).
     *
     * @return string
     */
    public function __toString()
    {
        return json_encode($this->toArray());
    }

    /**
     * Convert to an array.
     *
     * @return array
     */
    public function toArray()
    {
        return array(
            'name'     => $this->name,
            'source'   => $this->source,
            'coverage' => $this->coverage,
        );
    }

    // API

    /**
     * Add coverage.
     *
     * @param integer $lineNum Line number.
     * @param integer $count   Number of covered.
     * @return void
     */
    public function addCoverage($lineNum, $count)
    {
        $this->coverage[$lineNum] = $count;
    }

    // accessor

    /**
     * Return source filename.
     *
     * @return string
     */
    public function getName()
    {
        return $this->name;
    }

    /**
     * Return source content.
     *
     * @return string
     */
    public function getSource()
    {
        return $this->source;
    }

    /**
     * Return coverage data of the source file.
     *
     * @return array
     */
    public function getCoverage()
    {
        return $this->coverage;
    }

    /**
     * Return absolute path.
     *
     * @return string
     */
    public function getPath()
    {
        return $this->path;
    }

    /**
     * Return line number of the source file.
     *
     * @return integer
     */
    public function getFileLines()
    {
        return $this->fileLines;
    }
}

/**
 * Data represents "json_file" of Coveralls API.
 *
 * @author Kitamura Satoshi <[email protected]>
 */
class Coveralls
{
    /**
     * Service name.
     *
     * @var string
     */
    protected $serviceName;

    /**
     * Repository token.
     *
     * @var string
     */
    protected $repoToken;

    /**
     * Source files.
     *
     * @var SourceFile[]
     */
    protected $sourceFiles = array();

    /**
     * Constructor.
     *
     * @param string $serviceName Service name.
     * @param string $repoToken   Repo token.
     */
    public function __construct($serviceName = 'travis-ci', $repoToken = null)
    {
        $this->serviceName = $serviceName;
        $this->repoToken   = $repoToken;
    }

    /**
     * String expression (convert to json).
     *
     * @return string
     */
    public function __toString()
    {
        return json_encode($this->toArray());
    }

    /**
     * Convert to an array.
     *
     * @return array
     */
    public function toArray()
    {
        $files = array();

        foreach ($this->sourceFiles as $file) {
            $files[] = $file->toArray();
        }

        $data = array(
            'service_name' => $this->serviceName,
            'source_files' => $files,
        );

        if ($this->repoToken !== null) {
            $data['repo_token'] = $this->repoToken;
        }

        return $data;
    }

    // API

    /**
     * Add SourceFile.
     *
     * @param SourceFile $sourceFile
     */
    public function addSourceFile(SourceFile $sourceFile)
    {
        $this->sourceFiles[] = $sourceFile;
    }

    /**
     * Return whether the SourceFile object exists.
     *
     * @return boolean
     */
    public function hasSourceFiles()
    {
        return count($this->sourceFiles) > 0;
    }

    // accessor

    /**
     * Set service name.
     *
     * @param string $serviceName Service name.
     * @return Coveralls
     */
    public function setServiceName($serviceName)
    {
        $this->serviceName = $serviceName;

        return $this;
    }

    /**
     * Return service name.
     *
     * @return string.
     */
    public function getServiceName()
    {
        return $this->serviceName;
    }

    /**
     * Set repository token.
     *
     * @param string $repoToken Repository token.
     * @return Coveralls
     */
    public function setRepoToken($repoToken)
    {
        $this->repoToken = $repoToken;

        return $this;
    }

    /**
     * Return repository token.
     *
     * @return string
     */
    public function getRepoToken()
    {
        return $this->repoToken;
    }

    /**
     * Return source files.
     *
     * @return SourceFile[]
     */
    public function getSourceFiles()
    {
        return $this->sourceFiles;
    }
}

// collector

/**
 * Coverage collector for clover.xml.
 *
 * @author Kitamura Satoshi <[email protected]>
 */
class CloverXmlCoverageCollector
{
    // API

    /**
     * Collect coverage from XML object.
     *
     * @param SimpleXMLElement $xml  Clover XML object.
     * @param string           $root Path to src directory.
     * @return Coveralls
     */
    public function collect(SimpleXMLElement $xml, $root)
    {
        $coveralls = new Coveralls();

        foreach ($xml->project->package as $package) {
            foreach ($package->file as $file) {
                $srcFile = $this->collectFileCoverage($file, $root);

                if ($srcFile !== null) {
                    $coveralls->addSourceFile($srcFile);
                }
            }
        }

        return $coveralls;
    }

    // Internal method

    /**
     * Collect coverage data of a file.
     *
     * @param SimpleXMLElement $file Clover XML object of a file.
     * @param string           $root Path to src directory.
     * @return SourceFile
     */
    protected function collectFileCoverage(SimpleXMLElement $file, $root)
    {
        $fullpath = (string)$file['name'];

        if (false === $pos = strpos($fullpath, $root)) {
            return null;
        }

        $filename = str_replace($root, '', $fullpath);

        return $this->collectCoverage($file, $fullpath, $filename);
    }

    /**
     * Collect coverage data.
     *
     * @param SimpleXMLElement $file     Clover XML object of a file.
     * @param string           $path     Path to source file.
     * @param string           $filename Filename.
     * @return SourceFile
     */
    protected function collectCoverage(SimpleXMLElement $file, $path, $filename)
    {
        $srcFile = new SourceFile($path, $filename);

        foreach ($file->line as $line) {
            $lineNum = (int)$line['num'];

            if ($lineNum > 0) {
                $srcFile->addCoverage($lineNum - 1, (int)$line['count']);
            }
        }

        return $srcFile;
    }
}

// rest client

class RestClient
{
    public function upload($url, $path, $filename)
    {
        $post = array(
            $filename => '@' . $path,
        );

        $curl = curl_init();

        curl_setopt_array(
            $curl,
            array(
                CURLOPT_URL            => $url,
                CURLOPT_POST           => true,
                CURLOPT_POSTFIELDS     => $post,
                CURLOPT_RETURNTRANSFER => true,
            )
        );

        $data = curl_exec($curl);
        $info = curl_getinfo($curl);

        if ($info['http_code'] != 200) {
            $message = sprintf('Failed to call API. status code: %d', $info['http_code']);

            throw new \RuntimeException($message);
        }

        curl_close($curl);

        return $data;
    }
}

// run

$xmlFilename = "clover.xml";

$root = realpath(__DIR__ . "/..");
$logs = realpath("$root/build/logs");
$path = realpath("$logs/$xmlFilename");
$src  = "$root/src/";

if ($path === false || !file_exists($path)) {
    die("Not found $xmlFilename");
}

// collect coverage
$xml = simplexml_load_file($path);
$collector = new CloverXmlCoverageCollector();
$coveralls = $collector->collect($xml, $src);

// set token
$token = 'your-token-here';
$coveralls->setRepoToken($token);

// dump
$coverallsJson = "$logs/coveralls.json";
file_put_contents($coverallsJson, $coveralls);

// upload file
$url    = 'https://coveralls.io/api/v1/jobs';
$client = new RestClient();
$data   = $client->upload($url, $coverallsJson, 'json_file');