Add M+, M2+, M-H+, M+Na, M+NH4 adduct options to positive ion mode

[Copilot]

Adds five adduct options to positive ion mode as specified in the enviPat adduct table: M+ (molecular ion), M2+ (doubly charged), M-H+ (deprotonated cation), M+Na (sodium), and M+NH4 (ammonium).

Changes

• isolib.R: Added custom adduct definitions for M2+ and M-H+ (M+, M+Na, M+NH4 already exist in enviPat)

  • Definitions follow enviPat's 9-column format: Name, calc, Charge, Mult, Mass, Ion_mode, Formula_add, Formula_ded, Multi
  • Fixed formula modification logic that incorrectly assumed positive mode only uses Formula_add

• isolib.xml: Added 5 adduct options to positive mode dropdown, updated version to 2.6+galaxy4

• Tests: Added 5 test cases covering M+Na, M+NH4, M2+, M-H+, and multiple adducts

Bug Fix

The original logic caused hangs for positive mode adducts requiring formula deduction:

# Before: Positive mode always called mergeform
if (adduct$Ion_mode == "negative") {
    merged_chemforms <- enviPat::subform(...)
} else {
    merged_chemforms <- enviPat::mergeform(...)  # M-H+ failed here
}

# After: Check deduction first, independent of ion mode
if (adduct$Formula_ded != "FALSE") {
    merged_chemforms <- enviPat::subform(...)
} else if (adduct$Formula_add != "FALSE") {
    merged_chemforms <- enviPat::mergeform(...)
} else {
    merged_chemforms <- multiplied_chemforms
}

M-H+ requires deducting H in positive mode, which the original code couldn't handle.

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>isolib: provide more adduct options</issue_title>
<issue_description>Add more adduct options to the positive ion mode ([M]+, [M]2+, [M-H]+, [M+Na]+, [M+NH4]+) - all of these adducts have to be part of the table in https://rdrr.io/cran/enviPat/man/adducts.html

These have to be added in the Galaxy tool wrapper.

From the initial discussions, we concluded that it will be easiest to add the adducts manually for now and to have it fit the form of the enviPat adduct table, which has the following row layout:

Name                    calc                    Charge      Mult         Mass              Ion_mode     Formula_add Formula_ded Multi
2M+3H2O+2H     M+28.02312      1              2              28.02312000  positive        H8O6            FALSE           2

</issue_description>

<agent_instructions>make sure to also include a test for some of the more complex new adducts</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@acquayefrank For negative options, ask Elliot or Stepan.

Note that some options may not be supported.

• Fixes isolib: provide more adduct options #650

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