Fix output cheetah placeholders

[bernt-matthias]

Many tools use output names with invalid cheetah placeholders. Valid is ^[a-zA-Z_]\w*$.

A valid placeholder

• starts with a character or underscore
• and is followed by a sequence of alpha numeric characters or underscores

The following tools violate this (by starting with numbers or including dots). This should be fixed (please put your name / link to the PR next to the tool if you are working on this):

• tools/codeml/codeml.xml codeml: fix test parameters #4216
  • 2ngdn
  • 2ngds
  • 2ngt
  • 4fold
• tools/khmer/extract-partitions.xml
  • groups-of-partitions
• tools/medaka/medaka_variant.xml
  • out_round_1_phased.vcf
• tools/mothur/chimera.slayer.xml
  • slayer.chimeras
• tools/mothur/biom.info.xml
  • tax.summary
• tools/mothur/chimera.uchime.xml
  • uchime.chimeras
• tools/mothur/chimera.check.xml
  • chimeracheck.chimeras
• tools/mothur/chimera.bellerophon.xml
  • bellerophon.chimeras
  • bellerophon.accnos
• tools/mothur/chimera.pintail.xml
  • pintail.chimeras
• tools/mothur/chimera.vsearch.xml
  • vsearch.chimeras
• tools/mothur/chimera.ccode.xml
  • ccode.chimeras
  • ccode.accnos
• tools/mothur/align.check.xml
  • align.check
• tools/mummer4/dnadiff.xml
  • 1delta
  • 1coords