X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=a174cce11a3b4c928c3b08a817d534ad149822bb;hb=134a9c1275862a6b3ea10a2c0f11965c0a535854;hp=22f5a97b498187b23b651695e8b3d9a1b8cef1f6;hpb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b;p=mothur.git diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp index 22f5a97..a174cce 100644 --- a/pipelinepdscommand.cpp +++ b/pipelinepdscommand.cpp @@ -355,10 +355,14 @@ bool PipelineCommand::parseCommand(string nextCommand, string& name, string& opt bool PipelineCommand::checkForValidAndRequiredParameters(string name, string options, map >& 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 validParameters = command->getValidParameters(); @@ -370,17 +374,21 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt map >::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); if (itMade == mothurMadeFiles.end()) { - m->mothurOut("You have the " + it->first + " listed as a mothurmade file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine(); - return true; + if ((name == "align.seqs") && (it->first == "candidate")) {} //do nothing about candidate + else { + m->mothurOut("You have the " + it->first + " listed as a mothurmade file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine(); + return true; + } } } } - + //is the command missing any required vector requiredParameters = command->getRequiredParameters(); @@ -399,7 +407,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt 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 @@ -410,7 +418,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) { mothurMadeFiles[itMade->first] = itMade->second; //adds any new types } - + return false; } catch(exception& e) { @@ -435,8 +443,8 @@ int PipelineCommand::runUsersPipeline(){ 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; } } @@ -525,8 +533,9 @@ int PipelineCommand::runUsersPipeline(){ } } //********************************************************************************************************************** -bool PipelineCommand::fillInMothurMade(string& options, map > mothurMadeFiles){ +bool PipelineCommand::fillInMothurMade(string& options, map >& mothurMadeFiles){ try { + OptionParser parser(options); map parameters = parser.getParameters(); map::iterator it; @@ -536,21 +545,28 @@ bool PipelineCommand::fillInMothurMade(string& options, mapsecond == "mothurmade") { - itMade = mothurMadeFiles.find(it->first); + string paraType = it->first; + string tempOption = it->second; + + if (tempOption == "mothurmade") { + + if (it->first == "candidate") { paraType = "fasta"; } + + itMade = mothurMadeFiles.find(paraType); if (itMade == mothurMadeFiles.end()) { - m->mothurOut("Looking for a mothurmade " + it->first + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine(); + m->mothurOut("Looking for a mothurmade " + paraType + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine(); return true; }else{ vector temp = itMade->second; if (temp.size() > 1) { //ask user which file to use - m->mothurOut("More than one file has been created for the " + it->first + " parameter. "); m->mothurOutEndLine(); + m->mothurOut("More than one file has been created for the " + paraType + " parameter. "); m->mothurOutEndLine(); for (int i = 0; i < temp.size(); i++) { m->mothurOut(toString(i) + " - " + temp[i]); m->mothurOutEndLine(); } + m->mothurOut("Please select the number of the file you would like to use: "); int num = 0; cin >> num; @@ -558,23 +574,43 @@ bool PipelineCommand::fillInMothurMade(string& options, map (temp.size()-1))) { m->mothurOut("Not a valid response, quitting."); m->mothurOutEndLine(); return true; } else { - parameters[it->first] = temp[num]; + tempOption = temp[num]; } //clears buffer so next command doesn't have error string s; getline(cin, s); + vector newTemp; + for (int i = 0; i < temp.size(); i++) { + if (i == num) { newTemp.push_back(temp[i]); } + else { + m->mothurOut("Would you like to remove " + temp[i] + " as an option for " + paraType + ", (y/n): "); m->mothurOutEndLine(); + string response; + cin >> response; + m->mothurOutJustToLog(response); m->mothurOutEndLine(); + + if (response == "n") { newTemp.push_back(temp[i]); } + + //clears buffer so next command doesn't have error + string s; + getline(cin, s); + } + } + + mothurMadeFiles[paraType] = newTemp; + + }else if (temp.size() == 0){ - m->mothurOut("Sorry, we seem to think you created a " + it->first + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine(); + m->mothurOut("Sorry, we seem to think you created a " + paraType + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine(); return true; }else{ - parameters[it->first] = temp[0]; + tempOption = temp[0]; } } } - options += it->first + "=" + parameters[it->first] + ", "; + options += it->first + "=" + tempOption + ", "; } //rip off extra comma @@ -594,13 +630,13 @@ void PipelineCommand::createPatsPipeline(){ //sff.info command string thisCommand = "sffinfo(sff=" + sffFile + ")"; - //commands.push_back(thisCommand); + commands.push_back(thisCommand); //trim.seqs command string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta"; string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual"; - //thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")"; - //commands.push_back(thisCommand); + thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")"; + commands.push_back(thisCommand); //unique.seqs string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";