I have find the solution i made a mistake in my config.xml file.
We have to define the mail template like this
<template>
<email>
<{section_name}_{group_name}_{fields_name} translate="label" module="mymodule">
<label>Custom Email Template</label>
<file>mymodule/custom_email.html</file>
<type>html</type>
</{section_name}_{group_name}_{fields_name}>
</email>
</template>
{section_name} {group_name} {fields_name} in system.xml file.
Cheers