Maximum m/z in compute-fragmentation-trees

[helenamrusso]

@anupriyatripathi @ElDeveloper There is a limit of m/z in the compute-fragmentation-trees step. It should be interesting to increase this value (maybe to ~m/z 1200 or so?) since some groups can be characterized by several glycosyl units, for instance.

_qiime qemistree compute-fragmentation-trees \ --i-features Malpighiaceae_Filtered_EtOH80_NEG_Sirius_MergeMSMS.mgf.qza \ --p-sirius-path 'sirius-osx64-headless-4.0.1/bin' \ --p-n-jobs 8 \ --p-ppm-max 20 \ --p-profile qtof \ --p-maxmz 1000 \ --p-ionization-mode negative \ --p-java-flags '-Djava.io.tmpdir=/Users/helenarusso/ -Xms45G -Xmx60G' \ --o-fragmentation-trees Malpighiaceae_EtOH80_NEG_fragmentation_treestest1000.qza \ --verbose

If we put a value above 850, we get an error:

bash: line 2: activate: No such file or directory Traceback (most recent call last): File "/Users/helenarusso/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call results = action(arguments) File "</Users/helenarusso/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-211>", line 2, in compute_fragmentation_trees File "/Users/helenarusso/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 208, in bound_callable self.signature.check_types(user_input) File "/Users/helenarusso/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/core/type/signature.py", line 354, in check_types % (name, parameter, spec.qiime_type)) TypeError: Parameter 'maxmz' received 1000 as an argument, which is incompatible with parameter type: Int % Range(100, 850, inclusive_end=True)

Plugin error from qemistree:

Parameter 'maxmz' received 1000 as an argument, which is incompatible with parameter type: Int % Range(100, 850, inclusive_end=True)

See above for debug info.

[ElDeveloper]

Looks like @anupriyatripathi closed this issue in #144. Thanks both!