Mercurial > repos > goeckslab > cell_intensity_processing
changeset 4:5d541df02496 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5cf3005f482381216061eb8718aba8f5c8bcb0d5
| author | goeckslab |
|---|---|
| date | Fri, 10 May 2024 21:01:41 +0000 |
| parents | 4f5abe01531c |
| children | |
| files | macros.xml process_intensities.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/macros.xml Fri May 10 17:52:26 2024 +0000 +++ b/macros.xml Fri May 10 21:01:41 2024 +0000 @@ -16,6 +16,6 @@ </xml> <token name="@TOOL_VERSION@">0.0.1</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <token name="@PROFILE@">19.01</token> </macros>
--- a/process_intensities.xml Fri May 10 17:52:26 2024 +0000 +++ b/process_intensities.xml Fri May 10 21:01:41 2024 +0000 @@ -30,12 +30,12 @@ AF_markers = [x for x in list(marker_df['${AF_method.AF_col}'].unique()) if x != 'None'] print(f'Detected {quant[AF_markers].eq(0.0).any(axis=1).sum()} cells with AF values of zero in the dataset') -#if $AF_filter == 'filter': +#if $AF_method.AF_filter == 'filter': pre_filter_count = len(quant) quant = quant.loc[quant[AF_markers].ne(0.0).any(axis=1),:] print(f'Filtered out {pre_filter_count - len(quant)} cells that had AF values of 0.0') -#elif $AF_filter == 'clip': +#elif $AF_method.AF_filter == 'clip': print('Clipping all AF values equal to 0.0 to the minimum non-zero AF value') for af in AF_markers: quant[af] = quant[af].clip(lower = quant[af][quant[af].ne(0.0)].min())