Use multiple file selector instead of repeating single file selector.

Thanks to John Chilton (@jmchilton) for explaining how this works,
and updating the Galaxy documentation for the Tool Config Syntax:
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Use Biopython 1.62 rather than 1.61; Fix dependency for get_orfs_or_cdss
Tabs to spaces in get_orfs_or_cdss.xml
Close this XML tag directly
Tabs to 4 spaces in seq_rename.xml
Tabs to 4 spaces in seq_filter_by_id.xml
Tabs to 4 spaces in seq_select_by_id.xml