add rules for new panel processing

src/depiction_targeted_preproc/workflow/Snakefile

@@ -2,6 +2,7 @@ version: "3"
 
 
 include: "rules/rules_prepare_pipeline.smk"
+include: "rules/rules_panel.smk"
 include: "rules/rules_proc.smk"
 include: "rules/rules_vis.smk"
 include: "rules/rules_qc.smk"

src/depiction_targeted_preproc/workflow/rules/rules_panel.smk

@@ -0,0 +1,26 @@
+"""This file bundles all panel manipulation rules needed throughout the pipeline.
+To keep things tidy, each file will be in the same directory `{sample}/panels/`.
+Initially before the workflow is started a file `mass_list.raw.csv` has to be created.
+"""
+
+
+rule panel_standardized_full:
+    input:
+        csv="{sample}/panels/unstandardized_full.csv",
+    output:
+        csv="{sample}/panels/full.csv",
+    shell:
+        "python -m depiction_targeted_preproc.workflow.panel.standardize_panel "
+        "--input-panel-path {input.csv} --config-name standardize_main_config.yml "
+        "--output-panel-path {output.csv}"
+
+
+rule panel_filter_calibration:
+    input:
+        csv="{sample}/panels/full.csv",
+    output:
+        csv="{sample}/panels/calibration.csv",
+    run:
+        import polars as pl
+
+        pl.read_csv(input.csv).filter(type="target").write_csv(output.csv)