Complete gzipped FASTA query support

[peterjc]

Pull request #102 added partial support for gzipped FASTA files as -query and -subject, but not all the tools use this. e.g. ncbi_blastn_wrapper.xml:

#if $query.is_of_type('fasta.gz'):
-query <(gunzip -c '${query}')
#else:
-query '${query}'
#end if

and:

<param argument="-query" type="data" format="fasta,fasta.gz" label="Nucleotide query sequence(s)"/>

But ncbi_blastp_wrapper.xml and ncbi_tblastn_wrapper.xml etc have:

-query '$query'

and:

<param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/>

We should make the (nucleotide and protein) query parameters into a pair of macros, and the command line snippet into a third macro.

NOTE: The Cheetah snippet will break on older versions of Galaxy and wrongly try to gunzip plain FASTA files, see galaxyproject/tools-iuc#1373 - this has been fixed in galaxyproject/galaxy#4224 and back ported to Galaxy release 16.07 galaxyproject/galaxy#4230

[peterjc]

Should be fixed with b555967 and 935d782

Also c42e1f6 adds a workaround for old Galaxy wrongly using gunzip all the time.

I will release this today as v0.3.1