--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment_size_distribution.xml	Mon Aug 20 12:39:15 2018 -0400
@@ -0,0 +1,28 @@
+<tool id="alignment_size_distribution" name="Create size distribution for alignment files" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="6.7">click</requirement>
+        <requirement type="package" version="0.23">pandas</requirement>
+        <requirement type="package" version="0.15">pysam</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution'
+    ]]></command>
+    <inputs>
+        <param name="alignment_file" type="data" format="bam,unsorted.bam"/>
+        <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/>
+        <param argument="--maximum_size" type="integer" value="18" min="1" label="Maximum read length to consider"/>
+        <param argument="--wide" type="boolean" checked="false" truevalue="--wide" label="Output wide instead of long tabular format"/>
+    </inputs>
+    <outputs>
+        <data name="distribution" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignment_file" value="test_data.bam" ftype="bam"/>
+            <output name="distribution" value="distribution.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Generates a table with reference sequence, sense and antisense counts.
+    ]]></help>
+</tool>