//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
// 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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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);
}
}