- CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose);
- CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet);
- CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion);
- CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed);
- CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom);
- CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle);
- CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor);
- CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen);
- CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist);
- CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA);
- CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein);
- CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes);
- CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura);
- CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout);
- CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees);
- CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
+ CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
+ CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
+ CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
+ CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
+ CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
+ CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
+ CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
+ CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
+ CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
+ CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
+ CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
+ CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
+ CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
+ CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);