add collection_type to input collection in JBrowse2 (bgruening#1485)

* 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

* update help
some prompts
add bgperpx - todo add as a parameter

* 2.12.2 update
Add wiggle track colour and other controls
Add bpPerPx in advanced section to control view scale at default open
Clarify dependence on remote URI tabix data if uri source used.

* bump to 2.12.3 jb2
still passes tests - no breakage yet.

* fix JB2VER although not currently used...

* Have the no-build plugin for bed colour above and below zero binary working!
Involved a substantial simplification of the default_session setup - just needed "configuration": displayId in the display.
Simples.

* remove copy for strings.

* Update tools/jbrowse2/jbrowse2.xml

Co-authored-by: Björn Grüning <[email protected]>

* Update tools/jbrowse2/jbrowse2.xml

Co-authored-by: Björn Grüning <[email protected]>

* fix flake errors and some suggestions

* thought I'd got this one...

* add the new plugin js

* change bed default to not use plugin

* add help explaining relationship to the Bigwig extremes to bed features tool and to the advanced control form.

* update to 2.13.0 release
fix biotools jbrowse entry
informative error message if collection has no fasta reference

* decrement version suffix back to zero

* remove flakery spaces

* make genome from history and built in genome non-optional to fix a sentry issue reported and PR suggested by Marius

* update to 2.13.1 opportunistically :)

* Add collection_type to input collection. It should always be a list

<param name="autoCollection" type="data_collection" collection_type="list" label="Collection of bed, bam and other track files"/>

Suggestion from Marius - thanks!

---------

Co-authored-by: Björn Grüning <[email protected]>

tools/jbrowse2/macros.xml

@@ -101,7 +101,7 @@
                     <option value="collect">Convert a collection of suitable track files</option>
                 </param>
                 <when value="collect">
-                    <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
+                    <param name="autoCollection" type="data_collection" collection_type="list" label="Collection of bed, bam and other track files"/>
                 </when>
                 <when value="form"/>
             </conditional>