modify.js

function modify(modifiers) {

    return through2.obj(function(file, encoding, done) {

        var stream = this;

        function applyModifiers(content) {
            (typeof modifiers === 'function' ? [modifiers] : modifiers).forEach(function(modifier) {
                content = modifier(content, file);
            });
            return content;
        }

        function write(data) {
            file.contents = new Buffer(data);
            stream.push(file);
            done();
        }

        if (file.isBuffer()) {
            write(applyModifiers(String(file.contents)));
        } else if (file.isStream()) {
            var buffer = '';
            file.contents.on('data', function(chunk) {
                buffer += chunk;
            });
            file.contents.on('end', function() {
                write(applyModifiers(String(buffer)));
            });
        }
    });
}

task.js

gulp.src('app.js')
    .pipe(modify(version))
    .pipe(modify(swapStuff))
    .pipe(gulp.dest('build/'));

function version(data) {
    return data.replace(/__VERSION__/, '0.0.1');
}

function swapStuff(data) {
    return data.replace(/(\w+)\s(\w+)/, '$2, $1');
}