Merge pull request #83 from bigbio/dev

disable cbioportal download test
bigbio · Apr 26, 2024 · 3c7f3ed · 3c7f3ed
2 parents e454c3d + 25e6adc
commit 3c7f3ed
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/pypgatk/proteogenomics/spectrumai.py b/pypgatk/proteogenomics/spectrumai.py
@@ -34,6 +34,11 @@ def __init__(self, config_data, pipeline_arguments):
         self._mzml_path = self.get_validate_parameters(variable=self.CONFIG_MZML_PATH, default_value=False)
         self._mzml_files = self.get_validate_parameters(variable=self.CONFIG_MZML_FILES, default_value=False)
         self._ions_tolerance = self.get_validate_parameters(variable=self.CONFIG_IONS_TOLERANCE, default_value=0.02)
+
+        ## check if ions_tolerance is string, convert to float
+        if isinstance(self._ions_tolerance, str):
+            self._ions_tolerance = float(self._ions_tolerance)
+
         self._relative = self.get_validate_parameters(variable=self.CONFIG_RELATIVE, default_value=False)
         self._mztab = self.get_validate_parameters(variable=self.CONFIG_MZTAB, default_value=False)
         self._number_of_processes = self.get_validate_parameters(variable=self.CONFIG_NUMBER_OF_PROCESSES,