On Thu, Sep 22, 2011 at 9:14 AM, Timothy Wu <2hug...@gmail.com> wrote:
> Hi,
> I'm implementing my own tools. In one tool I may have hundreds of input
> files.

That will be tricking in Galaxy - and unless there is some clever
functionality I'm not aware of, very tedious for the end user. I
think they'd have to manually select each file from a combo
box (drop down select menu). Even if a single multi-select
combobox could be used (can it? not sure off hand), it would
be easy to make a mistake and miss out a file.

How does your tool handle this at the command line (ignoring Galaxy)?
Does it expect a directory name or pattern, or just a really long
command line string with many many file names?

> ... I'm also curious if there is a limit to how long the command can
> be at the shell level. I suspect the tool won't be able to run especially
> with each of the galaxy files is designated in the absolute path.

Yes, there is an OS specific limit to the length of a command line string.

If you do simply have hundreds of filenames in the command line string,
you are likely to hit this limit - especially with absolute paths.

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