- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
- CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
- CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
- CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
+ CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+ CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
+ CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);