Generate ISO for El Capitan from App Store without any 3rd party tools, I've tested it on Yosemite, most of the credits go to Gabriel L. Somlo

generateiso.py

#!/usr/bin/python
import subprocess
import sys
import struct

def pbzx():
    if sys.stdin.read(4) != "pbzx":
        print "Not a pbzx stream"
        sys.exit(1)

    flags = struct.unpack(">Q", sys.stdin.read(8))[0]

    while (flags & 1 << 24):
        flags, length = struct.unpack(">QQ", sys.stdin.read(16))
        xz = None
        while length:
            xbuf = sys.stdin.read(min(4*1024, length))
            if xz == None:
                xz = xbuf[:8] == "\xfd7zXZ\x00\x00\x00"
                if xz:
                    p = subprocess.Popen("zcat", stdin=subprocess.PIPE)
            length -= len(xbuf)
            if xz:
                p.stdin.write(xbuf)
            else:
                sys.stdout.write(xbuf)
        if xz:
            p.stdin.close()
            p.wait()
        # This is required because Popen seems to flush stdout
        sys.stdout.flush()

def main():
    subprocess.check_call('''
NAME="El Capitan"
# Mount the installer image:
hdiutil attach "/Applications/Install OS X $NAME.app/Contents/SharedSupport/InstallESD.dmg" -noverify -nobrowse -mountpoint /Volumes/install_app

# Convert the boot image to a sparse bundle:
hdiutil convert /Volumes/install_app/BaseSystem.dmg -format UDSP -o "/tmp/$NAME"

# Increase the sparse bundle capacity for packages, kernel, etc.:
hdiutil resize -size 8g "/tmp/$NAME.sparseimage"

# Mount the sparse bundle target for further processing:
hdiutil attach "/tmp/$NAME.sparseimage" -noverify -nobrowse -mountpoint /Volumes/install_build

# Remove Package link and replace with actual files:
rm /Volumes/install_build/System/Installation/Packages
cp -rp /Volumes/install_app/Packages /Volumes/install_build/System/Installation/

# NEW: As of Yosemite, there are additional installer dependencies:
cp -rp /Volumes/install_app/BaseSystem* /Volumes/install_build/

# NEW: As of Yosemite, we also need a kernel image!
tar -Oxf /Volumes/install_app/Packages/Essentials.pkg Payload|python generateiso.py pbzx|tar -xC/Volumes/install_build/ ./System/Library/Kernels

# Unmount both the installer image and the target sparse bundle:
hdiutil detach /Volumes/install_app
hdiutil detach /Volumes/install_build

# Resize the partition in the sparse bundle to remove any free space:
hdiutil resize -size $(hdiutil resize -limits "/tmp/$NAME.sparseimage" | tail -n 1 | awk '{ print $1 }')b "/tmp/$NAME.sparseimage"

# Convert the sparse bundle to ISO/CD master:
hdiutil convert "/tmp/$NAME.sparseimage" -format UDTO -o "/tmp/$NAME"

# Remove the sparse bundle:
rm "/tmp/$NAME.sparseimage"

# Rename the ISO and move it to the desktop:
mv "/tmp/$NAME.cdr" "$HOME/Desktop/$NAME.iso"
''', shell=True)

if __name__ == "__main__":
    if len(sys.argv) > 1 and sys.argv[1] == 'pbzx': pbzx()
    else: main()