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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Shared pep box #2354

Closed Alexander-Sol closed 9 months ago

Alexander-Sol commented 9 months ago

Same as PR #2353, but the tick box behavior matches that of other LFQ tick boxes. And a tooltip was added.

Important back and forth on twitter today about the inclusion of shared peptides for label free quant. General sentiment is no, which has been the default parameter that we use in MetaMorpheus for flashlfq. However, the flashlfq app gives the user the option. Therefore I added a checkbox to the quantification section of the search task that allows the user to choose. The default is still to not include them.

codecov[bot] commented 9 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.64%. Comparing base (1085594) to head (a68a2b7).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2354/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2354?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2354 +/- ## ======================================= Coverage 92.64% 92.64% ======================================= Files 136 136 Lines 21229 21232 +3 Branches 2928 2928 ======================================= + Hits 19668 19671 +3 Misses 1083 1083 Partials 478 478 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2354?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2354?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1Bvc3RTZWFyY2hBbmFseXNpc1Rhc2suY3M=) | `93.36% <100.00%> (+<0.01%)` | :arrow_up: | | [...aMorpheus/TaskLayer/SearchTask/SearchParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2354?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1NlYXJjaFBhcmFtZXRlcnMuY3M=) | `100.00% <100.00%> (ø)` | |