view test-data/biosample.source @ 9:d20ab289b0c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"

if (package == "soil") {
	out << "#MIMARKS.survey.soil.4.0" << endl;
	 if (requiredonly) {
		out << "#{sample name}	{description of sample}	{sample title}	{description of library_construction_protocol}	{http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}" << endl;
		out << "#{text}	{text}	{text}	{text}	{controlled vacabulary}" << endl;
		out << "*sample_name	*description	*sample_title	*seq_methods	*organism" << endl;
	}else {
		out << "#{sample name}	{description of sample}	{sample title}	{description of library_construction_protocol}	{http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}	{soil classification from the FAO World Reference Database for Soil Resources}" << endl;
		out << "#{text}	{text}	{text}	{text}	{controlled vacabulary}	{{term}}" << endl;
		out << "*sample_name	*description	*sample_title	*seq_methods	*organism	fao_class" << endl;
	}
}

if ((package == "soil") ) {}

vector<string> requiredFieldsForPackage;
requiredFieldsForPackage.push_back("sample_name");
requiredFieldsForPackage.push_back("description");
requiredFieldsForPackage.push_back("sample_title");
requiredFieldsForPackage.push_back("seq_methods");
requiredFieldsForPackage.push_back("organism");


if (packageType == "MIMARKS.survey.soil.4.0") {}