PipelineCommand::PipelineCommand(string option) {
try {
cFactory = CommandFactory::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
try {
m->mothurOut("The pipeline command is designed to guide you through your analysis using mothur.\n");
m->mothurOut("The pipeline command parameters are pipeline, sff, oligos, align, chimera, classify, taxonomy and processors.\n");
- m->mothurOut("The sff parameter allows you to enter your sff file. It is required.\n");
- m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required.\n");
- m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required.\n");
- m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required.\n");
- m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required.\n");
- m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required.\n");
+ m->mothurOut("The sff parameter allows you to enter your sff file. It is required, if not using pipeline parameter.\n");
+ m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required, if not using pipeline parameter.\n");
+ m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required, if not using pipeline parameter.\n");
+ m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required, if not using pipeline parameter.\n");
+ m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required, if not using pipeline parameter.\n");
+ m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required, if not using pipeline parameter.\n");
m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("The pipeline parameter allows you to enter your own pipeline file. This file should look like a mothur batchfile, but where you would be using a mothur generated file, you can use mothurmade instead.\n");
- m->mothurOut("First column contains the command name, and the second column contains the parameter options or 'defaults', meaning use defaults. You may leave out file options.\n");
m->mothurOut("Example: trim.seqs(processors=8, allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, fasta=may1.v13.fasta, oligos=may1.v13.oligos, qfile=may1.v13.qual)\n");
m->mothurOut("then, you could enter unique.seqs(fasta=mothurmade), and mothur would use the .trim.fasta file from the trim.seqs command. \n");
m->mothurOut("then you could enter align.seqs(candidate=mothurmade, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n");
int PipelineCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
bool PipelineCommand::checkForValidAndRequiredParameters(string name, string options, map<string, vector<string> >& mothurMadeFiles){
try {
+
+ if (name == "system") { return false; }
if (name == "system") { return false; }
//get shell of the command so we can check to make sure its valid without running it
Command* command = cFactory->getCommand(name);
-
+
//check to make sure all parameters are valid for command
vector<string> validParameters = command->getValidParameters();
map<string, vector<string> >::iterator itMade;
for (it = parameters.begin(); it != parameters.end(); it++) {
+
if (validParameter.isValidParameter(it->first, validParameters, it->second) != true) { return true; } // not valid
if (it->second == "mothurmade") {
itMade = mothurMadeFiles.find(it->first);
}
}
}
-
+
//is the command missing any required
vector<string> requiredParameters = command->getRequiredParameters();
if (!hasOr) { m->mothurOut(name + " requires the " + requiredParameters[i] + " parameter, please correct."); m->mothurOutEndLine(); }
}
}
-
+
// if all are needed and not all are found
if ((!hasOr) && (numFound != requiredParameters.size())) { return true; }
//if one is needed and none are found
for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
mothurMadeFiles[itMade->first] = itMade->second; //adds any new types
}
-
+
return false;
}
catch(exception& e) {
CommandOptionParser parser(nextCommand);
string commandName = parser.getCommandString();
string options = parser.getOptionString();
-
- if (options != "") {
+
+ if ((options != "") && (commandName != "system")) {
bool error = fillInMothurMade(options, mothurMadeFiles);
if (error) { in.close(); return 0; }
}
}
in.close();
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "PipelineCommand", "runUsersPipeline");
//**********************************************************************************************************************
bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<string> >& mothurMadeFiles){
try {
+
OptionParser parser(options);
map<string, string> parameters = parser.getParameters();
map<string, string>::iterator it;
projects / mothur.git / blobdiff