Hello,
1. How to define a character used at the beginning of a comment for ourput file. i.e. if "#" is used at the start of the comment Galaxy recognises this, but what if I want to use some other character.
is it possible to define this inside <outputs>    ?
<outputs>
    <data name="output" format="custom_format" label="${input.name}_mappedreads.yyy"> </data>

</outputs>

2. How does the "Number of comment lines" populated in the file properties ? (form where does Galaxy get this information from when the "auto detect button is pressed" ?)

Regards,
Sabry.