# HG changeset patch
# User goeckslab
# Date 1715374901 0
# Node ID 5d541df02496f7b008ae7446bff297d9aa885098
# Parent  4f5abe01531c078e426bc832fc7483fb10b55c63
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5cf3005f482381216061eb8718aba8f5c8bcb0d5

diff -r 4f5abe01531c -r 5d541df02496 macros.xml
--- 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>
diff -r 4f5abe01531c -r 5d541df02496 process_intensities.xml
--- 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())