Link software items to gene and pilot report pdf files

[Nicklas Nordborg]

When starting the gene report and pilot report wizards it should be possible to select a software item that represents the current version of the R report script.

If the usual selections lists are going to be used we need to specify new software types.

Hmmm... by using the ParameterSet annotation (see #629) on the software item it would even be possible to configure multiple settings for <gene-report>/<pilot-report>. For example:

<pilot-report>
   <!-- the current version -->
   <path>...</path>
   <!-- older versions -->
   <path parameter-set="v1.0">...</path>
   <path parameter-set="v2.0">...</path>
...
</pilot-report>

Then, by selecting a matching software item it would be possible to use the specified version of the report script.

NOTE! Due to how the current auto-confirmation system, counters, etc are implemented parameter-set is not supported on the <pdf-name> setting.

[Nicklas Nordborg]

(In [3616]) References #830: Link software items to gene and pilot report pdf files

Added Report subtype and ReportTemplate annotation type for software. The ReportTemplate annotation is an enum that can be either GENE_REPORT or PILOT_REPORT.

Matching software items can be selected in the 'Gene report' and 'Pilot report' wizards.

[Nicklas Nordborg]

(In [3618]) References #830: Link software items to gene and pilot report pdf files

Added support for selecting software when starting the GeneReportPlugin. It will present a list of software items filtered by type=REPORT_SOFTWARE and ReportTemplate=GENE_REPORT|PILOT_REPORT. The default software is determined by whatever that is set as the project default.

The selected software item is linked from the generated file using an any-to-any link.

When using the AutoConfirm the project default software is always selected.

[Nicklas Nordborg]

(In [3620]) References #830: Link software items to gene and pilot report pdf files

Added support for ParameterSet annotation. It only works on leaf nodes in the configuration:

<gene-report>
  <path parameter-set="v1.0">...</path>
  <path>...</path>
</gene-report>

ParameterSet is igored on <pdf-name> since it would make it very messy with auto-confirmation, counters, etc. which assumes that all reports of the same type have the same file name.