# HG changeset patch
# User mvdbeek
# Date 1524937878 14400
# Node ID 7fd65542efc2ec5212fc21cd18681932620af7d6
# Parent  427f5dda88547006b1965e4c3f13cff16c82958d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b

diff -r 427f5dda8854 -r 7fd65542efc2 average_scores.xml
--- a/average_scores.xml	Fri Apr 27 14:54:05 2018 -0400
+++ b/average_scores.xml	Sat Apr 28 13:51:18 2018 -0400
@@ -11,32 +11,37 @@
 import pandas as pd
 
 #set files = [str(f) for f in $input_files]
-#set column = 3 if $input_files[0].ext in ['bed', 'bedgraph'] else 5
+#set column = {'bed': 4, 'bedgraph': 3, 'gff': 5, 'gff3': 5, 'gtf': 5}[$input_files[0].ext]
+skiprows = 0
+with open('$files[0]') as first_file:
+    for i, line in enumerate(first_file):
+        if not line.startswith(('track', 'browser', '#')):
+            skiprows = i
+            break
 d = {}
 #for f in $files:
-d['$f'] = pd.read_csv('$f', usecols=[$column], sep="\t", skiprows=$skiprows, header=None, squeeze=True)
+d['$f'] = pd.read_csv('$f', usecols=[$column], sep="\t", skiprows=skiprows, header=None, squeeze=True)
 #end for
 df = pd.DataFrame.from_dict(d)
 mean = df.mean(axis=1)
 with open('$averaged_output', 'w') as out, open('$files[0]') as first_file:
     for i, line in enumerate(first_file):
         fields = line.strip().split("\t")
-        if i >= $skiprows:
-            fields[$column] = str(mean[i - $skiprows])
+        if i >= skiprows:
+            fields[$column] = str(mean[i - skiprows])
         out.write("%s\n" % "\t".join(fields))
     </configfile>
 </configfiles>
     <inputs>
         <param name="input_files" type="data" multiple="true" format="bed,bedgraph,gff" label="Select the files for which to average the score"/>
-        <param name="skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="To skip comments and track definition lines"/>
     </inputs>
     <outputs>
         <data name="averaged_output" format_source="input_files" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_files" value="1.bed,2.bed" ftype="bed"/>
-            <output name="averaged_output" value="averaged.bed" ftype="bed"/>
+            <param name="input_files" value="1.bed,2.bed" ftype="bedgraph"/>
+            <output name="averaged_output" value="averaged.bed" ftype="bedgraph"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 427f5dda8854 -r 7fd65542efc2 test-data/1.bed
--- a/test-data/1.bed	Fri Apr 27 14:54:05 2018 -0400
+++ b/test-data/1.bed	Sat Apr 28 13:51:18 2018 -0400
@@ -1,3 +1,4 @@
+track type=bedGraph name="test"
 X	23522161	23522595	0
 X	23522595	23522617	0
 X	23522617	23522667	0
diff -r 427f5dda8854 -r 7fd65542efc2 test-data/2.bed
--- a/test-data/2.bed	Fri Apr 27 14:54:05 2018 -0400
+++ b/test-data/2.bed	Sat Apr 28 13:51:18 2018 -0400
@@ -1,3 +1,4 @@
+track type=bedGraph name="test"
 X	23522161	23522595	0
 X	23522595	23522617	0
 X	23522617	23522667	0
diff -r 427f5dda8854 -r 7fd65542efc2 test-data/averaged.bed
--- a/test-data/averaged.bed	Fri Apr 27 14:54:05 2018 -0400
+++ b/test-data/averaged.bed	Sat Apr 28 13:51:18 2018 -0400
@@ -1,3 +1,4 @@
+track type=bedGraph name="test"
 X	23522161	23522595	0.0
 X	23522595	23522617	0.0
 X	23522617	23522667	0.0