- OUTPUT("Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
- + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
- + "stockholm (sto, stk),\n" + "pir (pir),\n" + "blc (blc),\n"
- + "amsa (amsa),\n" + "json (json),\n" + "pileup (pileup),\n"
- + "msf (msf),\n" + "clustal (aln),\n" + "phylip (phy),\n"
- + "jalview (jvp, jar).", Opt.STRING, Opt.LINKED,
- Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, Opt.REQUIREINPUT,
- Opt.OUTPUT),
- FORMAT("Sets the format for the preceding --output file. Valid formats are:\n"
- + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n" + "blc,\n"
- + "amsa,\n" + "json,\n" + "pileup,\n" + "msf,\n" + "clustal,\n"
- + "phylip,\n" + "jalview.", Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
- GROOVY("Process a groovy script in the file for the open alignment.",
+ OUTPUT(Type.OUTPUT,
+ "Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
+ + "stockholm (sto, stk),\n" + "pir (pir),\n"
+ + "blc (blc),\n" + "amsa (amsa),\n" + "json (json),\n"
+ + "pileup (pileup),\n" + "msf (msf),\n"
+ + "clustal (aln),\n" + "phylip (phy),\n"
+ + "jalview (jvp, jar).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
+ Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
+ FORMAT(Type.OUTPUT,
+ "Sets the format for the preceding --output file. Valid formats are:\n"
+ + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
+ + "blc,\n" + "amsa,\n" + "json,\n" + "pileup,\n"
+ + "msf,\n" + "clustal,\n" + "phylip,\n" + "jalview.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ GROOVY(Type.PROCESS,
+ "Process a groovy script in the file for the open alignment.",