diff test-data/biosample.source @ 0:7bfd66707e6f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:54:35 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosample.source	Tue Mar 20 21:54:35 2018 -0400
@@ -0,0 +1,24 @@
+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") {}