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shuzhao-li-lab / PythonCentricPipelineForMetabolomics

Python pipeline for metabolomics data preprocessing, QC, standardization and annotation
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Reset command example #68

Closed gmhhope closed 4 months ago

gmhhope commented 4 months ago

Reset command

Hi Josh,

I need to have an example of the reset command as the initial attempt fails and it complains the reset in not a valid subcommand.

My pcpfm version is: '1.0.9'.

(base) MLG-JGM357:~ gongm$ pcpfm reset -i /Users/gongm/Documents/projects/Adriana_U01_RZV_imm_persist/git-repo/output/pfmRun0508/HILICpos/
reset is not a valid subcommand
valid commands include:
     QAQC
     asari
     assemble
     assemble_study
     batch_correct
     blank_masking
     build_empCpds
     convert
     delete
     download_extras
     drop_missing_features
     drop_outliers
     drop_samples
     finish
     generate_output
     impute
     l1a_annotate
     l1b_annotate
     l2_annotate
     l4_annotate
     log_transform
     map_ms2
     normalize
     preprocess
     process_params
     report
     summarize

Thanks for the help in advance!

Best regards, Minghao

gmhhope commented 4 months ago

Upgrading to '1.0.14' still not working

jmmitc06 commented 4 months ago

This has been fixed in v1.0.15, the main function was improperly indented in main.