Mercurial > repos > iuc > mothur_rename_seqs

comparison test-data/biosample.source @ 0:1ac1d3e02088 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:01:03 -0400
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-1:000000000000 0:1ac1d3e02088
1 if (package == "soil") {
2 out << "#MIMARKS.survey.soil.4.0" << endl;
3 if (requiredonly) {
4 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;
5 out << "#{text} {text} {text} {text} {controlled vacabulary}" << endl;
6 out << "*sample_name *description *sample_title *seq_methods *organism" << endl;
7 }else {
8 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;
9 out << "#{text} {text} {text} {text} {controlled vacabulary} {{term}}" << endl;
10 out << "*sample_name *description *sample_title *seq_methods *organism fao_class" << endl;
11 }
12 }
13
14 if ((package == "soil") ) {}
15
16 vector<string> requiredFieldsForPackage;
17 requiredFieldsForPackage.push_back("sample_name");
18 requiredFieldsForPackage.push_back("description");
19 requiredFieldsForPackage.push_back("sample_title");
20 requiredFieldsForPackage.push_back("seq_methods");
21 requiredFieldsForPackage.push_back("organism");
22
23
24 if (packageType == "MIMARKS.survey.soil.4.0") {}