//********************************************************************************************************************** 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> 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); } }
//********************************************************************************************************************** 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); } }
//********************************************************************************************************************** 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> AlignCommand::setParameters(){ try { CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate); CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate); CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch); CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize); CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch); CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign); CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch); CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen); CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip); CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold); 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, "AlignCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> ClassifyOtuCommand::setParameters(){ try { CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist); CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","constaxonomy",false,true,true); parameters.push_back(ptaxonomy); CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy); 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 ppersample("persample", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppersample); CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "","",false,false); parameters.push_back(pbasis); CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff); CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs); 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, "ClassifyOtuCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> MGClusterCommand::setParameters(){ try { CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast); CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength); CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty); CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff); CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision); CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod); CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard); CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin); CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge); CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster); 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, "MGClusterCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** 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); } }
//********************************************************************************************************************** vector<string> ClusterCommand::setParameters(){ try { CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip); CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname); CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount); CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",false,false,true); parameters.push_back(pcolumn); CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff); CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false,true); parameters.push_back(pmethod); CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund); CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim); CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust); 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, "ClusterCommand", "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> SRACommand::setParameters(){ try { CommandParameter psff("sff", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(psff); CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup); CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos); CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfile); CommandParameter pfastq("fastq", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfastq); //choose only one multiple options CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform); CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs); CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs); CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs); CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs); CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs); //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, "SRACommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** 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> 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); } }
//********************************************************************************************************************** vector<string> SffMultipleCommand::setParameters(){ try { CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfile); //sffinfo CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim); //trim.flows CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop); CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows); CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows); CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs); CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs); CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs); CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs); CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs); CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal); CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise); CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder); //shhh.flows CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup); CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff); CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter); CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge); CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma); CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta); //trim.seqs parameters CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles); CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pflip); CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig); CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength); CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength); CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepforward); CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pkeepfirst); CommandParameter premovelast("removelast", "Number", "", "0", "", "", "","",false,false); parameters.push_back(premovelast); 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, "SffMultipleCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> GetCurrentCommand::setParameters(){ try { CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); 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, "GetCurrentCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> LoadLogfileCommand::setParameters(){ try { CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plogfile); 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, "LoadLogfileCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** 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); } }
//********************************************************************************************************************** vector<string> SetLogFileCommand::setParameters(){ try { CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend); CommandParameter pname("name", "String", "", "", "", "", "","",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, "SetLogFileCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> PCOACommand::setParameters(){ try { CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip); CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric); 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, "PCOACommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> GetSAbundCommand::setParameters(){ try { CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist); CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund); 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, "GetSAbundCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> MakeFileCommand::setParameters(){ try { CommandParameter ptype("type", "Multiple", "fastq-gz", "fastq", "", "", "","",false,false); parameters.push_back(ptype); CommandParameter pnumcols("numcols", "Multiple", "2-3", "3", "", "", "","",false,false, true); parameters.push_back(pnumcols); 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, "MakeFileCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** vector<string> OtuHierarchyCommand::setParameters(){ try { CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput); CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist); 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, "OtuHierarchyCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** 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); } }
//********************************************************************************************************************** vector<string> SetDirectoryCommand::setParameters(){ try { CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault); CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput); CommandParameter poutput("output", "String", "", "", "", "", "",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, "SetDirectoryCommand", "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> RemoveDistsCommand::setParameters(){ try { CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "PhylipColumn", "none","phylip",false,false,true); parameters.push_back(pphylip); CommandParameter pcolumn("column", "InputTypes", "", "", "none", "PhylipColumn", "none","column",false,false,true); parameters.push_back(pcolumn); CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos); 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, "RemoveDistsCommand", "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> 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); } }
//********************************************************************************************************************** vector<string> AnosimCommand::setParameters(){ try { CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pdesign); CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pphylip); CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha); 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, "AnosimCommand", "setParameters"); exit(1); } }
//********************************************************************************************************************** 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); } }