jbrowse2: fix for pif; deprecate blastxml (bgruening#1529)

* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker
It actually does work. Sort of.
Hope this is useful to someone.

* fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :)

* add yara mapper ToolFactory - NOT from nf-core.
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

* small test files still work :)

* single quotes for $runme - disappeared mysteriously :(

* adding panaroo

* Finally fixed the '$runme' suggestion and got the sanitisers not to.

* fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement...

* cleanup master branch of fork

* Idiotic sort error generates broken pif indexes.
Pity the built in fails in biocontainers.

* problem with pif
revert to paf until sorted

* return to using paf unindexed until figure out why the jbrowse utility is broken
tabix does not do this.

* remove tabix code - won't work.

* remove debug ls

* flake8

* Remove blastxml - current GFF parser refuses to display the output from the
old JB1 converter so deprecating everything

Fixes to pif finally working
Turns out that the SHELL env variable must be set when calling
jbrowse command line functions to
prevent node.js from asking for some ID which does not end well
in the bare bones biocontainer.

* remove blastxml related deprecated scripts