--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/average_scores.xml	Fri Apr 27 14:54:05 2018 -0400
@@ -0,0 +1,49 @@
+<tool id="average_score" name="Calculate average scores" version="0.1.3">
+    <description>for fixed step interval files</description>
+    <requirements>
+        <requirement type="package" version="0.22">pandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$average_script'
+    ]]></command>
+<configfiles>
+    <configfile name="average_script">
+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
+d = {}
+#for f in $files:
+d['$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 - $skiprows])
+        out.write("%s\n" % "\t".join(fields))
+    </configfile>
+</configfiles>
+    <inputs>
+        <param name="input_files" type="data" multiple="true" format="bed,bedgraph,gff" label="Select the files for which to average the score"/>
+        <param name="skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="To skip comments and track definition lines"/>
+    </inputs>
+    <outputs>
+        <data name="averaged_output" format_source="input_files" label="${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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+------------
+
+This tool calculates the average value for the score column across many datasets.
+
+        ]]></help>
+</tool>