# HG changeset patch
# User mvdbeek
# Date 1546938114 18000
# Node ID edca422b6cd6480ea1980547b8d9760831b686a9
# Parent  3fd7995da4fd4a08c416cbc59d00f0ce12a3e879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit 77e1df794a4bceebf80dc0d800c18577c531a277

diff -r 3fd7995da4fd -r edca422b6cd6 damid_deseq2_to_peaks.py
--- a/damid_deseq2_to_peaks.py	Mon Jan 07 12:58:55 2019 -0500
+++ b/damid_deseq2_to_peaks.py	Tue Jan 08 04:01:54 2019 -0500
@@ -26,7 +26,7 @@
 def significant_gatcs_to_peaks(df, p_value_cutoff):
     # Add `pass` column for sig. GATCs
     df['pass'] = 0
-    df.loc[df[6] < p_value_cutoff, 'pass'] = 1
+    df.loc[(df[6] < p_value_cutoff) & (df[2] > 0), 'pass'] = 1
     # Create pass_id column for consecutive pass or no-pass GATCs
     # True whenever there is a value change (from previous value):
     df['pass_id'] = df.groupby('chr')['pass'].diff().ne(0).cumsum()
diff -r 3fd7995da4fd -r edca422b6cd6 test-data/peaks.bed
--- a/test-data/peaks.bed	Mon Jan 07 12:58:55 2019 -0500
+++ b/test-data/peaks.bed	Tue Jan 08 04:01:54 2019 -0500
@@ -1,2 +1,1 @@
 4	1	251
-4	301	501
diff -r 3fd7995da4fd -r edca422b6cd6 test-data/test_data.tab
--- a/test-data/test_data.tab	Mon Jan 07 12:58:55 2019 -0500
+++ b/test-data/test_data.tab	Tue Jan 08 04:01:54 2019 -0500
@@ -3,5 +3,5 @@
 4_201_251	169.22778018355	5.7093345566596	0.605350118969888	9.43145855224256	4.0442550874846e-21	1.15555073230549e-17
 4_251_276	169.22778018355	5.7093345566596	0.605350118969888	9.43145855224256	4.0442550874846e-21	1.15555073230549e-1
 4_276_301	169.22778018355	5.7093345566596	0.605350118969888	9.43145855224256	4.0442550874846e-21	1.15555073230549e-1
-4_301_401	412.221939093451	4.95034623243659	0.53002737065317	9.33979357770923	9.65221128246454e-21	2.46758781436206e-17
-4_401_501	165.881402812843	5.71524958810642	0.620499842499124	9.21071883771587	3.23948149277376e-20	6.66609779385658e-17
+4_301_401	412.221939093451	-4.95034623243659	0.53002737065317	9.33979357770923	9.65221128246454e-21	2.46758781436206e-17
+4_401_501	165.881402812843	-5.71524958810642	0.620499842499124	9.21071883771587	3.23948149277376e-20	6.66609779385658e-17