Poor error message on nearly-complete pruning on Collapse

[davideby]

This was reported by Michael Reich. There's an odd corner case with an unintended error message for a Collapse that results in a nearly-complete (but not *totally-complete) pruning:

openjdk version "11.0.3" 2019-04-16
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.3+7)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.3+7, mixed mode)
WARNING: package com.apple.laf not in java.desktop
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
java.lang.IllegalArgumentException: numMarkers: 100 cannot be larger than dataset size: 6
	at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.markers.PermutationTest.<init>(PermutationTest.java:70)
	at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:117)
	at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:82)
	at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:91)
	at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:103)
	at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:166)
	at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:401)
	at org.gsea_msigdb.gsea/org.genepattern.modules.GseaWrapper.main(GseaWrapper.java:291)
	at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:29)

What's happening here is that the collapsed dataset is not empty but since the number of remaining features is less than the default setting for the Number of Markers parameter, we end up with a numMarkers error instead of a "pruning" error.

The pruning error message is bad enough, but this is even more obscure. It would be good to somehow detect when this happens as a result of Collapse and to give an appropriate message.