Closed ridderl closed 11 years ago
ridderl
commented
11 years ago Choosing a formula tree should result in all precision parameters to be set to 0 (mz_precision, mz_precision_abs, precursor_mz_precision) Choosing a mass tree should also result in precursor_mz_precision to be set to 0 (but not mz_precision, mz_precision_abs) It would be convenient if the form fields that are put to 0 when choosing the Tree format are dynamically removed from the Form Panel.
ridderl
commented
11 years ago What do you think about the idea to include "Formula Tree" in the pull down menu and add _neg or _pos based on the ionisation mode selected in the Annotate box? (Forgot to mention this idea on the phone, sorry)
ridderl
commented
11 years ago Reopened, see comments on required changes in precision parameters and the question about the possibility to couple the choice in formula tree with the ionisation mode.
sverhoeven
commented
11 years ago On the web form I can give mzxml, mass_tree and formula_tree as MS data formats. During construction of the magma job command line arguments I can look at the ionisation and alter the format when it's set to formula_tree.
ridderl
commented
11 years ago Yes that is what I meant: would be perfect
ridderl
commented
11 years ago The precision settings still need to be set to zero, see top comment
ridderl
commented
11 years ago Almost perfect! One minor detail: the behavior for Formula Tree and Mass Tree need to be swapped ...
ridderl
commented
11 years ago _neg is not added to form_tree in the script
Job has the following ms_data_formats: ["mzxml", "mass_tree","form_tree_pos","form_tree_neg"]
For interpreting the tree based on formula's it is necessary to know the ionization mode and should be consistent with the annotate option. So, ideally, only 3 formats should be exposed on the website: mzXML, Mass Tree, Formula Tree The choice between "form_tree_pos","form_tree_neg" should be determined on the basis of the Annotate option "Ionisation mode"