Beispiel #1
0
//**********************************************************************************************************************
vector<string> HeatMapCommand::setParameters(){	
	try {
		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);	
		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
		CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
		CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
		CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "HeatMapCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> ClassifyRFSharedCommand::setParameters(){	
	try {
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);		
        CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);	
        CommandParameter potupersplit("otupersplit", "Multiple", "log2-squareroot", "log2", "", "", "","",false,false); parameters.push_back(potupersplit);
        CommandParameter psplitcriteria("splitcriteria", "Multiple", "gainratio-infogain", "gainratio", "", "", "","",false,false); parameters.push_back(psplitcriteria);
		CommandParameter pnumtrees("numtrees", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pnumtrees);
        CommandParameter pdopruning("prune", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdopruning);
        CommandParameter ppruneaggrns("pruneaggressiveness", "Number", "", "0.9", "", "", "", "", false, false); parameters.push_back(ppruneaggrns);
        CommandParameter pdiscardhetrees("discarderrortrees", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdiscardhetrees);
        CommandParameter phetdiscardthreshold("errorthreshold", "Number", "", "0.4", "", "", "", "", false, false); parameters.push_back(phetdiscardthreshold);
        CommandParameter psdthreshold("stdthreshold", "Number", "", "0.0", "", "", "", "", false, false); parameters.push_back(psdthreshold);
         CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "ClassifySharedCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> RemoveGroupsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);	        
        CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "RemoveGroupsCommand", "setParameters");
		exit(1);
	}
}
Beispiel #4
0
//**********************************************************************************************************************
vector<string> TreeGroupCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false,true); parameters.push_back(pshared);
		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip);
		CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname);
		CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount);
        CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",false,false); parameters.push_back(pcolumn);		
        CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
        CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
		CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);		
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
		
        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "TreeGroupCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> RareFactCommand::setParameters(){	
	try {
		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-shannonrange", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
		CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
        CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "RareFactCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> SetCurrentCommand::setParameters(){	
	try {
		
		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 pfile("file", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfile);
        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 psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
		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 pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconstaxonomy);
        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontigsreport);
		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 pcurrent("current", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcurrent);
		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 pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "SetCurrentCommand", "setParameters");
		exit(1);
	}
}
Beispiel #7
0
//**********************************************************************************************************************
vector<string> GetRelAbundCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
		CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);
		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "GetRelAbundCommand", "setParameters");
		exit(1);
	}
}
Beispiel #8
0
//**********************************************************************************************************************
vector<string> CatchAllCommand::setParameters(){	
	try {
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		//can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
		CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(pshared);
		CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(psabund);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "CatchAllCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> MergeGroupsCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
		CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "MergeGroupsCommand", "setParameters");
		exit(1);
	}
}
Beispiel #10
0
//**********************************************************************************************************************
vector<string> CollectSharedCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
		CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
		CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
		CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "CollectSharedCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> KruskalWallisCommand::setParameters(){
	try {
        CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
        CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses);
        //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "KruskalWallisCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> GetMetaCommunityCommand::setParameters(){
	try {
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
        CommandParameter pminpartitions("minpartitions", "Number", "", "5", "", "", "","",false,false,true); parameters.push_back(pminpartitions);
        CommandParameter pmaxpartitions("maxpartitions", "Number", "", "100", "", "", "","",false,false,true); parameters.push_back(pmaxpartitions);
        CommandParameter poptimizegap("optimizegap", "Number", "", "3", "", "", "","",false,false,true); parameters.push_back(poptimizegap);
        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
   		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "NewCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> CooccurrenceCommand::setParameters() {	
	try { 
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);		
		CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "","",false,false); parameters.push_back(pmetric);
		CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "","",false,false); parameters.push_back(pmatrix);
        CommandParameter pruns("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pruns);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);

		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "CooccurrenceCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> GetCoreMicroBiomeCommand::setParameters(){	
	try {
        CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
		CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
        CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
		CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "GetCoreMicroBiomeCommand", "setParameters");
		exit(1);
	}
}
Beispiel #15
0
//**********************************************************************************************************************
vector<string> SummaryCommand::setParameters() {
    try {
        CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true);
        parameters.push_back(plist);
        CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false);
        parameters.push_back(prabund);
        CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false);
        parameters.push_back(psabund);
        CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true);
        parameters.push_back(pshared);
        CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false);
        parameters.push_back(psubsample);
        CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false);
        parameters.push_back(piters);
        CommandParameter plabel("label", "String", "", "", "", "", "","",false,false);
        parameters.push_back(plabel);
        CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true);
        parameters.push_back(pcalc);
        CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false);
        parameters.push_back(pabund);
        CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false);
        parameters.push_back(psize);
        CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false);
        parameters.push_back(pgroupmode);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false);
        parameters.push_back(pinputdir);
        CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false);
        parameters.push_back(poutputdir);

        vector<string> myArray;
        for (int i = 0; i < parameters.size(); i++) {
            myArray.push_back(parameters[i].name);
        }
        return myArray;
    }
    catch(exception& e) {
        m->errorOut(e, "SummaryCommand", "setParameters");
        exit(1);
    }
}
Beispiel #16
0
//**********************************************************************************************************************
vector<string> CorrAxesCommand::setParameters(){	
	try {
		CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes);
		CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
		CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
		CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
		CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes);
		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
		CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "CorrAxesCommand", "setParameters");
		exit(1);
	}
}
Beispiel #17
0
//**********************************************************************************************************************
vector<string> MetaStatsCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
		CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "MetaStatsCommand", "setParameters");
		exit(1);
	}
}
Beispiel #18
0
//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "sharedFasta", "none", "none","fasta",false,false); parameters.push_back(pfasta);
		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "groupList","",false,false,true); parameters.push_back(pgroup);
		CommandParameter plist("list", "InputTypes", "", "", "sharedList", "sharedList", "groupList","sharedseq",false,false,true); parameters.push_back(plist);
        CommandParameter pshared("shared", "InputTypes", "", "", "sharedList-sharedFasta", "sharedList", "none","sharedseq",false,false,true); parameters.push_back(pshared);
		CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter puniquegroups("uniquegroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(puniquegroups);
		CommandParameter psharedgroups("sharedgroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(psharedgroups);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);

		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "GetSharedOTUCommand", "setParameters");
		exit(1);
	}
}
Beispiel #19
0
// Test Change.
//**********************************************************************************************************************
vector<string> NewCommand::setParameters(){	
	try {
		//eaxamples of each type of parameter. more info on the types of parameters can be found in commandparameter.h
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
        
        //files that have dependancies
        CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","outputType",false,false); parameters.push_back(pphylip);
		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","outputType",false,false); parameters.push_back(pname);
		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","outputType",false,false); parameters.push_back(pcolumn);		
        //files that do not have dependancies - fasta is set to not be required whereas shared is set to be required
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","outputType",false,false); parameters.push_back(pfasta);
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);		

        
        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		
        //choose more than one multiple options
        CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc);
        //choose only one multiple options
        CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "","",false,false); parameters.push_back(pdistance);
        
        CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
        
        //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "NewCommand", "setParameters");
		exit(1);
	}
}
Beispiel #20
0
//**********************************************************************************************************************
vector<string> RemoveRareCommand::setParameters(){	
	try {
		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
		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 pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
		CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);
		CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "RemoveRareCommand", "setParameters");
		exit(1);
	}
}
Beispiel #21
0
//**********************************************************************************************************************
vector<string> MergeGroupsCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
        CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "sharedGroup", "countfasta","count",false,false,true); parameters.push_back(pcount);
		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
        CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "countfasta","fasta",false,false,true); parameters.push_back(pfasta);
        CommandParameter pmethod("method", "Multiple", "sum-average-median", "sum", "", "", "","",false,false, true); parameters.push_back(pmethod);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "MergeGroupsCommand", "setParameters");
		exit(1);
	}
}
Beispiel #22
0
//**********************************************************************************************************************
vector<string> SparccCommand::setParameters(){
	try {
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter psamplings("samplings", "Number", "", "20", "", "", "","",false,false,false); parameters.push_back(psamplings);
        CommandParameter piterations("iterations", "Number", "", "10", "", "", "","",false,false,false); parameters.push_back(piterations);
        CommandParameter ppermutations("permutations", "Number", "", "1000", "", "", "","",false,false,false); parameters.push_back(ppermutations);
        CommandParameter pmethod("method", "Multiple", "relabund-dirichlet", "dirichlet", "", "", "","",false,false); parameters.push_back(pmethod);
        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); 
        //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "SparccCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
vector<string> ClassifySvmSharedCommand::setParameters() {
    try {
        //CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none", "summary", false, true, true);
        parameters.push_back(pshared);
        CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none", "", false, true, true);
        parameters.push_back(pdesign);

        // RFE or classification?
        // mode should be either 'rfe' or 'classify'
        CommandParameter mode("mode", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(mode);

        // cross validation parameters
        CommandParameter evaluationFoldCountParam("evaluationfolds", "Number", "", "3", "", "", "", "", false, false);
        parameters.push_back(evaluationFoldCountParam);
        CommandParameter trainingFoldCountParam("trainingfolds", "Number", "", "10", "", "", "", "", false, false);
        parameters.push_back(trainingFoldCountParam);

        CommandParameter smoc("smoc", "Number", "", "3", "", "", "", "", false, false);
        parameters.push_back(smoc);

        // Support Vector Machine parameters
        CommandParameter kernelParam("kernel", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(kernelParam);

        // data transformation parameters
        // transform should be 'zeroone' or 'zeromean' ('zeromean' is default)
        CommandParameter transformParam("transform", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(transformParam);

        CommandParameter verbosityParam("verbose", "Number", "", "0", "", "", "", "", false, false);
        parameters.push_back(verbosityParam);

        //CommandParameter potupersplit("otupersplit", "Multiple", "log2-squareroot", "log2", "", "", "","",false,false); parameters.push_back(potupersplit);
        //CommandParameter psplitcriteria("splitcriteria", "Multiple", "gainratio-infogain", "gainratio", "", "", "","",false,false); parameters.push_back(psplitcriteria);
        //CommandParameter pnumtrees("numtrees", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pnumtrees);

        // parameters related to pruning
        //CommandParameter pdopruning("prune", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdopruning);
        //CommandParameter ppruneaggrns("pruneaggressiveness", "Number", "", "0.9", "", "", "", "", false, false); parameters.push_back(ppruneaggrns);
        //CommandParameter pdiscardhetrees("discarderrortrees", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdiscardhetrees);
        //CommandParameter phetdiscardthreshold("errorthreshold", "Number", "", "0.4", "", "", "", "", false, false); parameters.push_back(phetdiscardthreshold);

        // want this parameter to behave like the one in classify.rf
        CommandParameter pstdthreshold("stdthreshold", "Number", "", "0.0", "", "", "", "", false, false);
        parameters.push_back(pstdthreshold);
        // pruning params end

        CommandParameter pgroups("groups", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(pgroups);
        CommandParameter plabel("label", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(plabel);
        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(pinputdir);
        CommandParameter poutputdir("outputdir", "String", "", "", "", "", "", "", false, false);
        parameters.push_back(poutputdir);

        vector<string> myArray;
        for (int i = 0; i < parameters.size(); i++) {
            myArray.push_back(parameters[i].name);
        }
        return myArray;
    }
    catch (exception& e) {
        m->errorOut(e, "ClassifySvmSharedCommand", "setParameters");
        exit(1);
    }
}