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 == "deconvolute") {
67 cout << "The deconvolute 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 deconvolute command parameter is fasta and it is required." << "\n";
71 cout << "The deconvolute command should be in the following format: " << "\n";
72 cout << "deconvolute(fasta=yourFastaFile) " << "\n";
73 }else if (globaldata->helpRequest == "dist.seq") {
74 cout << "The dist.seq command reads a file containing sequences and creates a distance file." << "\n";
75 cout << "The dist.seq command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors. " << "\n";
76 cout << "You must use one of the following parameters for your filename: fasta, phylip, clustal or nexus. " << "\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 ends 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.seq command should be in the following format: " << "\n";
82 cout << "dist.seq(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
83 cout << "Example dist.seq(fasta=amazon.fasta, calc=eachgap, ends=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 == "collect.single") {
86 cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
87 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";
88 cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n";
89 cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
90 cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
91 cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
92 cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson." << "\n";
93 validCalcs->printCalc("single", cout);
94 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
95 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
96 }else if (globaldata->helpRequest == "collect.shared") {
97 cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
98 cout << "The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use " << "\n";
99 cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
100 cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups)." << "\n";
101 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";
102 cout << "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
103 cout << "The default value for groups is all the groups in your groupfile." << "\n";
104 validCalcs->printCalc("shared", cout);
105 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
106 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";
107 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
108 }else if (globaldata->helpRequest == "get.group") {
109 cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
110 cout << "You may not use any parameters with the get.group command." << "\n";
111 cout << "The get.group command should be in the following format: " << "\n";
112 cout << "get.group()" << "\n";
113 cout << "Example get.group()." << "\n";
114 }else if (globaldata->helpRequest == "get.label") {
115 cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
116 cout << "You may not use any parameters with the get.label command." << "\n";
117 cout << "The get.label command should be in the following format: " << "\n";
118 cout << "get.label()" << "\n";
119 cout << "Example get.label()." << "\n";
120 }else if (globaldata->helpRequest == "get.line") {
121 cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
122 cout << "You may not use any parameters with the get.line command." << "\n";
123 cout << "The get.line command should be in the following format: " << "\n";
124 cout << "get.line()" << "\n";
125 cout << "Example get.line()." << "\n";
126 }else if (globaldata->helpRequest == "rarefaction.single") {
127 cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
128 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";
129 cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use " << "\n";
130 cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n";
131 cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
132 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";
133 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";
134 validCalcs->printCalc("rarefaction", cout);
135 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
136 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
137 }else if (globaldata->helpRequest == "rarefaction.shared") {
138 cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
139 cout << "The rarefaction.shared command parameters are label, line, iters, jumble, groups and calc. No parameters are required, but you may not use " << "\n";
140 cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
141 cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
142 cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, jumble=1, groups=B-C, calc=sharedobserved)." << "\n";
143 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";
144 cout << "The default value for groups is all the groups in your groupfile." << "\n";
145 validCalcs->printCalc("sharedrarefaction", cout);
146 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
147 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";
148 cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
149 }else if (globaldata->helpRequest == "summary.single") {
150 cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
151 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";
152 cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
153 cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
154 cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
155 cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
156 validCalcs->printCalc("summary", cout);
157 cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
158 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
159 cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
160 }else if (globaldata->helpRequest == "summary.shared") {
161 cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
162 cout << "The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use " << "\n";
163 cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
164 cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n";
165 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";
166 validCalcs->printCalc("sharedsummary", cout);
167 cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
168 cout << "The default value for groups is all the groups in your groupfile." << "\n";
169 cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
170 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";
171 cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
172 }else if (globaldata->helpRequest == "parsimony") {
173 cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
174 cout << "The parsimony command parameters are random, groups and iters. No parameters are required." << "\n";
175 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";
176 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";
177 cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
178 cout << "Example parsimony(random=out, iters=500)." << "\n";
179 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";
180 cout << "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual." << "\n";
181 cout << "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename)." << "\n" << "\n";
182 }else if (globaldata->helpRequest == "unifrac.weighted") {
183 cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
184 cout << "The unifrac.weighted command parameters are groups and iters. No parameters are required." << "\n";
185 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";
186 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";
187 cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
188 cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
189 cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
190 cout << "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual." << "\n";
191 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
192 }else if (globaldata->helpRequest == "unifrac.unweighted") {
193 cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
194 cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
195 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";
196 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";
197 cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
198 cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
199 cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
200 cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n";
201 cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
202 }else if (globaldata->helpRequest == "libshuff") {
203 cout << "The libshuff command can only be executed after a successful read.dist command." << "\n";
204 cout << "The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required." << "\n";
205 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";
206 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";
207 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";
208 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";
209 cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n";
210 cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n";
211 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";
212 cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
213 cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
214 }else if (globaldata->helpRequest == "heatmap") {
215 cout << "The heatmap command can only be executed after a successful read.otu command." << "\n";
216 cout << "The heatmap 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";
217 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
218 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";
219 cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
220 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";
221 cout << "The heatmap command should be in the following format: heatmap(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
222 cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
223 cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
224 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";
225 cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
226 cout << "The heatmap command outputs a .svg file for each line or label you specify." << "\n";
227 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
228 }else if (globaldata->helpRequest == "venn") {
229 cout << "The venn command can only be executed after a successful read.otu command." << "\n";
230 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";
231 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";
232 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";
233 cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
234 cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao)." << "\n";
235 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";
236 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";
237 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";
238 cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
239 cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
240 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
241 }else if (globaldata->helpRequest == "tree.shared") {
242 cout << "The tree.shared command can only be executed after a successful read.otu command." << "\n";
243 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";
244 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
245 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";
246 cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
247 cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
248 cout << "The default value for groups is all the groups in your groupfile." << "\n";
249 cout << "There is no default value for calc." << "\n";
250 validCalcs->printCalc("treegroup", cout);
251 cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
252 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
253 }else if (globaldata->helpRequest == "bootstrap.shared") {
254 cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
255 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";
256 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
257 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";
258 cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
259 cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
260 cout << "The default value for groups is all the groups in your groupfile." << "\n";
261 cout << "There is no default value for calc. The default for iters is 1000." << "\n";
262 validCalcs->printCalc("boot", cout);
263 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";
264 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
265 }else if (globaldata->helpRequest == "concensus") {
266 cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
267 cout << "The concensus command has no parameters." << "\n";
268 cout << "The concensus command should be in the following format: concensus()." << "\n";
269 cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
270 cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
271 cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
272 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";
273 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";
274 }else if (globaldata->helpRequest == "bin.seqs") {
275 cout << "The bin.seqs command can only be executed after a successful read.otu command of a list file." << "\n";
276 cout << "The bin.seqs command parameters are fasta, name, line and label. The fasta parameter is required, and you may not use line and label at the same time." << "\n";
277 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";
278 cout << "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, line=yourLines, label=yourLabels)." << "\n";
279 cout << "Example bin.seqs(fasta=amazon.fasta, line=1-3-5, name=amazon.names)." << "\n";
280 cout << "The default value for line and label are all lines in your inputfile." << "\n";
281 cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
282 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
283 }else if (globaldata->helpRequest == "get.oturep") {
284 cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
285 cout << "The get.oturep command parameters are list, fasta, name, line and label. The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
286 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";
287 cout << "The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, line=yourLines, label=yourLabels)." << "\n";
288 cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, line=1-3-5, name=amazon.names)." << "\n";
289 cout << "The default value for line and label are all lines in your inputfile." << "\n";
290 cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
291 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
292 }else if (globaldata->helpRequest == "quit") {
293 cout << "The quit command will terminate Dotur and should be in the following format: " << "\n";
294 cout << "quit()" << "\n" << "\n";
295 }else if (globaldata->helpRequest == "") {
296 validCommands->printCommands(cout);
297 cout << "For more information about a specific command type 'help(commandName)' i.e. 'help(read.dist)'" << endl;
299 cout << globaldata->helpRequest << " is not a valid command" << endl;
302 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";
306 //**********************************************************************************************************************/
projects / mothur.git / blob