Mercurial > repos > iuc > mothur_collect_shared
diff test-data/biosample.source @ 0:afac0d63dac6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:13:01 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosample.source Fri May 19 05:13:01 2017 -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") {}