Hi,

I am trying to write a wrapper to run blast on our servers, running it off the NCBI would be too slow.

I am beginning this process by looking at the galaxy tutorial

1) I got this GC content example to work. But was curious, in #3 Create Tool Definition of the url above,

<command interpreter="perl">toolExample.pl $input $output</command>

What does $input mean? Where is it coming from? It cannot come from <inputs> directly below this code, since there is a diff between inputs and input. I have galaxy with biolinux, so an explicit file would be wonderful.

P.S. I read pretty much all of the doc on galaxy. Coping and pasting a URL will not help. Please give me a clear example since I have a limited Comp sci background. Thanks!