This PR adds one new file type to both the spectral inputs and the PSM inputs. The new spectral file type is mzXML. I decided against adding the mgf file type for now due to difficulty in getting out the scan number from the header. The new PSM file type is an mzIdentML, but I did not make it the default yet, which remains the pepXML. I also added some tests for at the least the XML based file types.
This PR adds one new file type to both the spectral inputs and the PSM inputs. The new spectral file type is mzXML. I decided against adding the mgf file type for now due to difficulty in getting out the scan number from the header. The new PSM file type is an mzIdentML, but I did not make it the default yet, which remains the pepXML. I also added some tests for at the least the XML based file types.