コード例 #1
0
//**********************************************************************************************************************
vector<string> GetSeqsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
        CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "FNGLT", "none","fastq",false,false,true); parameters.push_back(pfastq);
        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
		CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
		CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
		CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
		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 paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);

		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, "GetSeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #2
0
ファイル: clearcutcommand.cpp プロジェクト: barrykui/mothur
//**********************************************************************************************************************
vector<string> ClearcutCommand::setParameters(){	
	try {
		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);
		
		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, "ClearcutCommand", "setParameters");
		exit(1);
	}
}
コード例 #3
0
ファイル: preclustercommand.cpp プロジェクト: YuJinhui/mothur
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
		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", "none", "none","",false,false,true); parameters.push_back(pgroup);
		CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
        CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false); parameters.push_back(palign);
        CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
        CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
        CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
        CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);

        CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);

		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, "PreClusterCommand", "setParameters");
		exit(1);
	}
}
コード例 #4
0
//**********************************************************************************************************************
vector<string> ChopSeqsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
        CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
        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", "none", "none","group",false,false,true); parameters.push_back(pgroup);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
        CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
		CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
		CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
		CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
        CommandParameter pkeepn("keepn", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pkeepn);
		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, "ChopSeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #5
0
//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
		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, "DeUniqueSeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #6
0
//**********************************************************************************************************************
vector<string> ReverseSeqsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); parameters.push_back(pqfile);
		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, "ReverseSeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #7
0
//**********************************************************************************************************************
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);
	}
}
コード例 #8
0
ファイル: makegroupcommand.cpp プロジェクト: campenr/mothur
//**********************************************************************************************************************
vector<string> MakeGroupCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
		CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
		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, "MakeGroupCommand", "setParameters");
		exit(1);
	}
}
コード例 #9
0
ファイル: seqsummarycommand.cpp プロジェクト: jklynch/mothur
//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
		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, "SeqSummaryCommand", "setParameters");
		exit(1);
	}
}
コード例 #10
0
ファイル: deconvolutecommand.cpp プロジェクト: mothur/mothur
//**********************************************************************************************************************
vector<string> DeconvoluteCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
        CommandParameter pformat("format", "Multiple", "count-name", "name", "", "", "","",false,false, true); parameters.push_back(pformat);
        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, "DeconvoluteCommand", "setParameters");
		exit(1);
	}
}
コード例 #11
0
//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
		CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
		CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
		CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
		CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
		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, "FilterSeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #12
0
//**********************************************************************************************************************
vector<string> ChimeraBellerophonCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
		CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
		CommandParameter pcorrection("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
		CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
		CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); 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, "ChimeraBellerophonCommand", "setParameters");
		exit(1);
	}
}
コード例 #13
0
//**********************************************************************************************************************
vector<string> ChimeraPerseusCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
		CommandParameter pcutoff("cutoff", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pcutoff);
		CommandParameter palpha("alpha", "Number", "", "-5.54", "", "", "",false,false); parameters.push_back(palpha);
		CommandParameter pbeta("beta", "Number", "", "0.33", "", "", "",false,false); parameters.push_back(pbeta);
			
		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, "ChimeraPerseusCommand", "setParameters");
		exit(1);
	}
}
コード例 #14
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);
	}
}
コード例 #15
0
ファイル: preclustercommand.cpp プロジェクト: barrykui/mothur
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){	
	try {
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
		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", "none", "none","",false,false,true); parameters.push_back(pgroup);
		CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
        CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);

		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, "PreClusterCommand", "setParameters");
		exit(1);
	}
}
コード例 #16
0
ファイル: newcommandtemplate.cpp プロジェクト: mothur/mothur
// 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);
	}
}
コード例 #17
0
ファイル: mergegroupscommand.cpp プロジェクト: mothur/mothur
//**********************************************************************************************************************
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);
	}
}
コード例 #18
0
//**********************************************************************************************************************
vector<string> ChimeraCheckCommand::setParameters(){	
	try {
		CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
		CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
		CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
		CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		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 psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);

		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, "ChimeraCheckCommand", "setParameters");
		exit(1);
	}
}
コード例 #19
0
ファイル: classifyseqscommand.cpp プロジェクト: mothur/mothur
//**********************************************************************************************************************
vector<string> ClassifySeqsCommand::setParameters(){	
	try {
		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
		CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
        CommandParameter poutput("output", "Multiple", "simple-detail", "detail", "", "", "","",false,false, true); parameters.push_back(poutput);
		CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
		CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
		CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
        CommandParameter pprintlevel("printlevel", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pprintlevel);
		CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
		CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
		CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
		CommandParameter pcutoff("cutoff", "Number", "", "80", "", "", "","",false,true); parameters.push_back(pcutoff);
		CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
		CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
        CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
        CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
		CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
		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, "ClassifySeqsCommand", "setParameters");
		exit(1);
	}
}
コード例 #20
0
//**********************************************************************************************************************
vector<string> ChimeraPintailCommand::setParameters(){	
	try {
		CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
		CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation);
		CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile);
		CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
		CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow);
		CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
		CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
		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);
		CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);

		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, "ChimeraPintailCommand", "setParameters");
		exit(1);
	}
}
コード例 #21
0
//**********************************************************************************************************************
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 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);
	}
}
コード例 #22
0
//**********************************************************************************************************************
vector<string> DistanceCommand::setParameters(){	
	try {
		CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn","column",false,false); parameters.push_back(pcolumn);
		CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn","",false,false); parameters.push_back(poldfasta);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true, true); parameters.push_back(pfasta);
		CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false, true); parameters.push_back(poutput);
		CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
		CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
		CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
		CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false, true); parameters.push_back(pcutoff);
		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, "DistanceCommand", "setParameters");
		exit(1);
	}
}
コード例 #23
0
ファイル: listseqscommand.cpp プロジェクト: mothur/mothur
//**********************************************************************************************************************
vector<string> ListSeqsCommand::setParameters(){	
	try {
        CommandParameter pfastq("fastq", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfastq);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
		CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
        CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
		CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
		CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
		CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
        CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
		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, "ListSeqsCommand", "setParameters");
		exit(1);
	}
}