diff --git a/cubi_isa_templates/isatab-somatic/cookiecutter.json b/cubi_isa_templates/isatab-somatic/cookiecutter.json index 1de41f1..9eda586 100644 --- a/cubi_isa_templates/isatab-somatic/cookiecutter.json +++ b/cubi_isa_templates/isatab-somatic/cookiecutter.json @@ -23,6 +23,10 @@ "exome sequencing", "genome sequencing" ], + "_measurement_type_terms": { + "exome sequencing": "http://purl.obolibrary.org/obo/OBI_0002118", + "genome sequencing": "http://purl.obolibrary.org/obo/OBI_0002117" + }, "lib_kit": [ "Agilent SureSelect Human All Exon V8", "Agilent SureSelect Human All Exon V7", diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp new file mode 100644 index 0000000..906d812 Binary files /dev/null and b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp differ diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt index 06c780c..a389e54 100644 --- a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt @@ -60,7 +60,7 @@ Study Factor Type Term Source REF STUDY ASSAYS Study Assay File Name a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt{% if cookiecutter.is_triplet == True %} a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt{% endif %} Study Assay Measurement Type {{cookiecutter.measurement_type}}{% if cookiecutter.is_triplet == True %} transcriptome profiling{% endif %} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0002118{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000424{% endif %} +Study Assay Measurement Type Term Accession Number {{cookiecutter._measurement_type_terms[cookiecutter.measurement_type]}}{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000424{% endif %} Study Assay Measurement Type Term Source REF OBI{% if cookiecutter.is_triplet == True %} OBI{% endif %} Study Assay Technology Type nucleotide sequencing{% if cookiecutter.is_triplet == True %} nucleotide sequencing{% endif %} Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000626{% endif %}