Top ! All is working fine. Thanks for your help.
So if someone is interesting, it's configured like that :
extcommands.xml :
<command>
<name>Ventilation 50%</name>
<execute>/var/lib/Repetier-Server/alveo/start50%.sh</execute>
<confirm>Démarrer ventilation à 50% ?</confirm>
<local>true</local>
<remote>true</remote>
<print-permission>true</print-permission>
</command>
script /var/lib/Repetier-Server/alveo/start50%.sh :
#!/bin/bash
echo -ne "start;" > /dev/ttyAMA0
sleep 3
echo -ne "pwm:50%;" > /dev/ttyAMA0