From cb53051c146cea4dfdc4b8dee54ce7ba2a29224d Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 20 Jun 2024 08:45:11 +0200 Subject: [PATCH] add commented out definition for timsTOF support --- .../workflow/rules/rules_proc.smk | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_proc.smk b/src/depiction_targeted_preproc/workflow/rules/rules_proc.smk index 5fb201f..457bf0b 100644 --- a/src/depiction_targeted_preproc/workflow/rules/rules_proc.smk +++ b/src/depiction_targeted_preproc/workflow/rules/rules_proc.smk @@ -22,6 +22,30 @@ rule proc_pick_peaks: " --output-imzml-path {output.imzml[0]}" +# TODO currently needed for peak picked data, e.g. from timsTOF +#rule proc_pick_peaks: +# input: +# imzml=multiext("{sample}/corrected.original",".imzML",".ibd"), +# config="{sample}/pipeline_params.yml", +# output: +# imzml=multiext("{sample}/corrected.peaks_all",".imzML",".ibd"), +# shell: +# "python -m depiction_targeted_preproc.workflow.proc.pick_peaks " +# " --input-imzml-path {input.imzml[0]} --config-path {input.config} " +# " --output-imzml-path {output.imzml[0]}" +# +# +## TODO very experimental to be removed later again +#rule proc_filter_peaks: +# input: +# imzml=multiext("{sample}/corrected.peaks_all",".imzML",".ibd"), +# output: +# imzml=multiext("{sample}/corrected.peaks",".imzML",".ibd"), +# shell: +# "python -m depiction_targeted_preproc.workflow.proc.filter_peaks " +# " --input-imzml-path {input.imzml[0]} " +# " --output-imzml-path {output.imzml[0]}" + # TODO this should be solved more efficiently in the future, but for now it is solved by calling the script twice rule proc_calibrate_remove_global_shift: input: