# HG changeset patch
# User mvdbeek
# Date 1524215466 14400
# Node ID 29f82a5c796696f98799b10fd8bb3eb58e3fc94a
# Parent  5a56b400df935134a2273302aae35eaf51e73278
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty

diff -r 5a56b400df93 -r 29f82a5c7966 damidseq_findpeaks.xml
--- a/damidseq_findpeaks.xml	Fri Apr 20 05:07:19 2018 -0400
+++ b/damidseq_findpeaks.xml	Fri Apr 20 05:11:06 2018 -0400
@@ -13,7 +13,7 @@
  --n=$n
  --step=$step
  --unified_peaks=$unified_peaks
- '$input_file' | LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' 2>&1 > log.txt&& 
+ '$input_file' | LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' 2>&1 | > log.txt && 
 mv peak_analysis*/*.gff peaks.gff &&
 cat peak_analysis*/*data >> log.txt
     ]]></command>
diff -r 5a56b400df93 -r 29f82a5c7966 log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/log	Fri Apr 20 05:11:06 2018 -0400
@@ -0,0 +1,20 @@
+Simple FDR random permutation peak caller
+Usage: [options] [files in bedgraph or GFF format]
+	
+Options:
+ --fdr            False discovery rate value
+                    [Current value: 0.01]
+ --frac           Number of random fragments to consider per iteration
+ --min_count      Minimum number of fragments to consider as a peak
+                    [Current value: 2]
+ --min_quant      Minimum quantile for considering peaks
+                    [Current value: 0.95]
+ --n              Number of iterations
+                    [Current value: 100]
+ --step           Stepping for quantiles
+                    [Current value: 0.01]
+ --unified_peaks  Method for calling peak overlaps (two options):
+                    'min': call minimum overlapping peak area
+                    'max': call maximum overlap as peak
+                    [Current value: max]
+