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!