5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "helpcommand.h"
12 //**********************************************************************************************************************
14 HelpCommand::HelpCommand(){
15 globaldata = GlobalData::getInstance();
16 validCommands = new ValidCommands();
17 validCalcs = new ValidCalculators();
20 //**********************************************************************************************************************
22 HelpCommand::~HelpCommand(){}
24 //**********************************************************************************************************************
26 int HelpCommand::execute(){
28 if (globaldata->helpRequest == "read.dist") {
29 cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
30 cout << "The read.dist command must be run before using the cluster or libshuff commands" << "\n";
31 cout << "The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command" << "\n";
32 cout << "For this use the read.dist command should be in the following format: " << "\n";
33 cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
34 cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n";
35 cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
36 cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n";
37 cout << "For this use the read.dist command should be in the following format: " << "\n";
38 cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n";
39 cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
40 }else if (globaldata->helpRequest == "read.otu") {
41 cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
42 cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
43 cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
44 cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
45 cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
46 cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
47 cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
48 cout << "The label and line parameters are used to read specific lines in your input." << "\n";
49 cout << "The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
50 cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n";
51 cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file" << "\n";
52 cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
53 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
54 }else if (globaldata->helpRequest == "read.tree") {
55 cout << "The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. " << "\n";
56 cout << "It also must be run before using the parsimony command, unless you are using the randomtree parameter." << "\n";
57 cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
58 cout << "The tree and group parameters are both required." << "\n";
59 cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
60 }else if (globaldata->helpRequest == "cluster") {
61 cout << "The cluster command can only be executed after a successful read.dist command." << "\n";
62 cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n";
63 cout << "The cluster command should be in the following format: " << "\n";
64 cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
65 cout << "The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed." << "\n" << "\n";
66 }else if (globaldata->helpRequest == "unique.seqs") {
67 cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
68 cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
69 cout << "If the sequence is unique the second column will just contain its name. " << "\n";
70 cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
71 cout << "The unique.seqs command should be in the following format: " << "\n";
72 cout << "unique.seqs(fasta=yourFastaFile) " << "\n";
73 }else if (globaldata->helpRequest == "dist.seqs") {
74 cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
75 cout << "The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. " << "\n";
76 cout << "The fasta parameter is required." << "\n";
77 cout << "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
78 cout << "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T." << "\n";
79 cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
80 cout << "The processors parameter allows you to specify number of processors to use. The default is 1, but you can use up to 4 processors." << "\n";
81 cout << "The dist.seqs command should be in the following format: " << "\n";
82 cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
83 cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3)." << "\n";
84 cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
85 }else if (globaldata->helpRequest == "align.seqs") {
86 cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
87 cout << "The align.seqs command parameters are fasta, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
88 cout << "The fasta and candidate parameters are required." << "\n";
89 cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer." << "\n";
90 cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman." << "\n";
91 cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n";
92 cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
93 cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n";
94 cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n";
95 cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n";
96 cout << "The align.seqs command should be in the following format: " << "\n";
97 cout << "align.seqs(fasta=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
98 cout << "Example align.seqs(candidate=candidate.fasta, fasta=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
99 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
100 }else if (globaldata->helpRequest == "collect.single") {
101 cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
102 cout << "The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
103 cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n";
104 cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
105 cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
106 cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
107 cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson." << "\n";
108 validCalcs->printCalc("single", cout);
109 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
110 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
111 }else if (globaldata->helpRequest == "collect.shared") {
112 cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
113 cout << "The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use " << "\n";
114 cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
115 cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups)." << "\n";
116 cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
117 cout << "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
118 cout << "The default value for groups is all the groups in your groupfile." << "\n";
119 validCalcs->printCalc("shared", cout);
120 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
121 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
122 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
123 }else if (globaldata->helpRequest == "get.group") {
124 cout << "The get.group command can only be executed after a successful read.otu command." << "\n";
125 //cout << "The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the concensus command." << "\n";
126 cout << "You may not use any parameters with the get.group command." << "\n";
127 cout << "The get.group command should be in the following format: " << "\n";
128 cout << "get.group()" << "\n";
129 cout << "Example get.group()." << "\n";
130 }else if (globaldata->helpRequest == "get.label") {
131 cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
132 cout << "You may not use any parameters with the get.label command." << "\n";
133 cout << "The get.label command should be in the following format: " << "\n";
134 cout << "get.label()" << "\n";
135 cout << "Example get.label()." << "\n";
136 }else if (globaldata->helpRequest == "get.line") {
137 cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
138 cout << "You may not use any parameters with the get.line command." << "\n";
139 cout << "The get.line command should be in the following format: " << "\n";
140 cout << "get.line()" << "\n";
141 cout << "Example get.line()." << "\n";
142 }else if (globaldata->helpRequest == "rarefaction.single") {
143 cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
144 cout << "The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
145 cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use " << "\n";
146 cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n";
147 cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
148 cout << "Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
149 cout << "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness." << "\n";
150 validCalcs->printCalc("rarefaction", cout);
151 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
152 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
153 }else if (globaldata->helpRequest == "rarefaction.shared") {
154 cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
155 cout << "The rarefaction.shared command parameters are label, line, iters, jumble, groups and calc. No parameters are required, but you may not use " << "\n";
156 cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
157 cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
158 cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, jumble=1, groups=B-C, calc=sharedobserved)." << "\n";
159 cout << "The default values for iters is 1000, jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n";
160 cout << "The default value for groups is all the groups in your groupfile." << "\n";
161 validCalcs->printCalc("sharedrarefaction", cout);
162 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
163 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
164 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
165 }else if (globaldata->helpRequest == "summary.single") {
166 cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
167 cout << "The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
168 cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
169 cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
170 cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
171 cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
172 validCalcs->printCalc("summary", cout);
173 cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
174 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
175 cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
176 }else if (globaldata->helpRequest == "summary.shared") {
177 cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
178 cout << "The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use " << "\n";
179 cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
180 cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n";
181 cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
182 validCalcs->printCalc("sharedsummary", cout);
183 cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
184 cout << "The default value for groups is all the groups in your groupfile." << "\n";
185 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
186 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
187 cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
188 }else if (globaldata->helpRequest == "parsimony") {
189 cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
190 cout << "The parsimony command parameters are random, groups and iters. No parameters are required." << "\n";
191 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group." << "\n";
192 cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
193 cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
194 cout << "Example parsimony(random=out, iters=500)." << "\n";
195 cout << "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony)," << "\n";
196 cout << "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual." << "\n";
197 cout << "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename)." << "\n" << "\n";
198 }else if (globaldata->helpRequest == "unifrac.weighted") {
199 cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
200 cout << "The unifrac.weighted command parameters are groups and iters. No parameters are required." << "\n";
201 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
202 cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
203 cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
204 cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
205 cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
206 cout << "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual." << "\n";
207 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
208 }else if (globaldata->helpRequest == "unifrac.unweighted") {
209 cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
210 cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
211 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group." << "\n";
212 cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
213 cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
214 cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
215 cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
216 cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n";
217 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
218 }else if (globaldata->helpRequest == "libshuff") {
219 cout << "The libshuff command can only be executed after a successful read.dist command." << "\n";
220 cout << "The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required." << "\n";
221 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
222 cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix." << "\n";
223 cout << "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form." << "\n";
224 cout << "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete." << "\n";
225 cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n";
226 cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n";
227 cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
228 cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
229 cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
230 }else if (globaldata->helpRequest == "heatmap.bin") {
231 cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
232 cout << "The heatmap.bin command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
233 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
234 cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n";
235 cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
236 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
237 cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
238 cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
239 cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
240 cout << "The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file." << "\n";
241 cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
242 cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
243 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
244 }else if (globaldata->helpRequest == "venn") {
245 cout << "The venn command can only be executed after a successful read.otu command." << "\n";
246 cout << "The venn command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
247 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups." << "\n";
248 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes." << "\n";
249 cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
250 cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao)." << "\n";
251 cout << "The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used." << "\n";
252 cout << "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups." << "\n";
253 cout << "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file." << "\n";
254 cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
255 cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
256 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
257 }else if (globaldata->helpRequest == "tree.shared") {
258 cout << "The tree.shared command can only be executed after a successful read.otu command." << "\n";
259 cout << "The tree.shared command parameters are groups, calc, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
260 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
261 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
262 cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
263 cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
264 cout << "The default value for groups is all the groups in your groupfile." << "\n";
265 cout << "There is no default value for calc." << "\n";
266 validCalcs->printCalc("treegroup", cout);
267 cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
268 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
269 }else if (globaldata->helpRequest == "dist.shared") {
270 cout << "The dist.shared command can only be executed after a successful read.otu command." << "\n";
271 cout << "The dist.shared command parameters are groups, calc, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
272 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
273 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like distance matrices created for, and are also separated by dashes." << "\n";
274 cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
275 cout << "Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
276 cout << "The default value for groups is all the groups in your groupfile." << "\n";
277 cout << "The default value for calc is jclass and thetayc." << "\n";
278 validCalcs->printCalc("matrix", cout);
279 cout << "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose." << "\n";
280 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
281 }else if (globaldata->helpRequest == "bootstrap.shared") {
282 cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
283 cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
284 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
285 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
286 cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
287 cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
288 cout << "The default value for groups is all the groups in your groupfile." << "\n";
289 cout << "There is no default value for calc. The default for iters is 1000." << "\n";
290 validCalcs->printCalc("boot", cout);
291 cout << "The bootstrap.shared command outputs a .tre file for each calculator you specify at each distance you choose containing iters number of trees." << "\n";
292 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
293 }else if (globaldata->helpRequest == "concensus") {
294 cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
295 cout << "The concensus command has no parameters." << "\n";
296 cout << "The concensus command should be in the following format: concensus()." << "\n";
297 cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
298 cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
299 cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
300 cout << "The .concensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the concensus tree " << "\n";
301 cout << "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages." << "\n" << "\n";
302 }else if (globaldata->helpRequest == "bin.seqs") {
303 cout << "The bin.seqs command can only be executed after a successful read.otu command of a list file." << "\n";
304 cout << "The bin.seqs command parameters are fasta, name, line, label and group. The fasta parameter is required, and you may not use line and label at the same time." << "\n";
305 cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
306 cout << "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
307 cout << "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
308 cout << "The default value for line and label are all lines in your inputfile." << "\n";
309 cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
310 cout << "If you provide a groupfile, then it also appends the sequences group to the name." << "\n";
311 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
312 }else if (globaldata->helpRequest == "filter.seqs") {
313 cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
314 cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical. " << "\n";
315 cout << "The fasta parameter is required." << "\n";
316 cout << "The trump parameter .... The default is ...." << "\n";
317 cout << "The soft parameter .... The default is ...." << "\n";
318 cout << "The hard parameter .... The default is ...." << "\n";
319 cout << "The vertical parameter .... The default is ...." << "\n";
320 cout << "The filter.seqs command should be in the following format: " << "\n";
321 cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
322 cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=...)." << "\n";
323 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
324 }else if (globaldata->helpRequest == "get.oturep") {
325 cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
326 cout << "The get.oturep command parameters are list, fasta, name, group, line and label. The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
327 cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
328 cout << "The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
329 cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
330 cout << "The default value for line and label are all lines in your inputfile." << "\n";
331 cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
332 cout << "If you provide a groupfile, then it also appends the names of the groups present in that bin." << "\n";
333 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
334 }else if (globaldata->helpRequest == "quit") {
335 cout << "The quit command will terminate mothur and should be in the following format: " << "\n";
336 cout << "quit()" << "\n" << "\n";
337 }else if (globaldata->helpRequest == "") {
338 validCommands->printCommands(cout);
339 cout << "For more information about a specific command type 'help(commandName)' i.e. 'help(read.dist)'" << endl;
341 cout << globaldata->helpRequest << " is not a valid command" << endl;
344 cout << endl << "For further assistance please refer to the Mothur manual on our wiki at http://schloss.micro.umass.edu/mothur/, or contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
348 //**********************************************************************************************************************/
projects / mothur.git / blob