expose out_type as normal user parameter (do not hide it as advanced)

cbielow · Oct 26, 2023 · 354cf8e · 354cf8e
1 parent af31eba
commit 354cf8e
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/topp/FileConverter.cpp b/src/topp/FileConverter.cpp
@@ -146,7 +146,7 @@ class TOPPFileConverter :
   void registerOptionsAndFlags_() override
   {
     registerInputFile_("in", "<file>", "", "Input file to convert.");
-    registerStringOption_("in_type", "<type>", "", "Input file type -- default: determined from file extension or content\n", false, true); // for TOPPAS
+    registerStringOption_("in_type", "<type>", "", "Input file type -- default: determined from file extension or content\n", false, false); // optional and not advanced (for workflow engines to show this param)
     vector<String> input_formats = {"mzML", "mzXML", "mgf", "raw", "cachedMzML", "mzData", "dta", "dta2d", "featureXML", "consensusXML", "ms2", "fid", "tsv", "peplist", "kroenik", "edta", "oms"};
     setValidFormats_("in", input_formats);
     setValidStrings_("in_type", input_formats);
@@ -158,7 +158,7 @@ class TOPPFileConverter :
     vector<String> output_formats = {"mzML", "mzXML", "cachedMzML", "mgf", "featureXML", "consensusXML", "edta", "mzData", "dta2d", "csv", "sqmass", "oms"};
     registerOutputFile_("out", "<file>", "", "Output file");
     setValidFormats_("out", output_formats);
-    registerStringOption_("out_type", "<type>", "", "Output file type -- default: determined from file extension or content\nNote: that not all conversion paths work or make sense.", false, true);
+    registerStringOption_("out_type", "<type>", "", "Output file type -- default: determined from file extension or content\nNote: that not all conversion paths work or make sense.", false, false); // optional and not advanced (for workflow engines to show this param)
     setValidStrings_("out_type", output_formats);
     registerFlag_("TIC_DTA2D", "Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions.", true);
     registerFlag_("MGF_compact", "Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)", true);