--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapping_quality_stats.xml	Wed Jun 15 10:43:07 2022 +0000
@@ -0,0 +1,62 @@
+<tool id="mapqstatistics" name="Mapping Quality Stats" version="0.16.0.1+galaxy0">
+  <description></description>
+  <requirements>
+        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement>
+        <requirement type="package" version="0.16.0.1">pysam</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+    ln -f -s $input.metadata.bam_index input.bam.bai &&
+    ln -s $input input.bam &&
+    python $__tool_directory__/mapping_quality_stats.py
+        -bam input.bam
+        -o $table &&
+    Rscript $__tool_directory__/mapping_quality_stats.r
+        -i '$table'
+        -o $plot
+  ]]></command>
+<inputs>
+    <param name="input" type="data" format="bam" label="Select a bam file to analyze"/>
+</inputs>
+
+ <outputs>
+   <data format="tabular" name="table" label="Distribution table" />
+   <data format="pdf" name="plot" label="Distribution of MAPQs" />
+</outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="sample.bam" ftype="bam"/>
+            <output file="distribution.tab" name="table" />
+            <output file="distribution.pdf" name="plot" />
+        </test>
+    </tests>
+
+
+<help>
+
+**What it does**
+
+Collects the values of mapping quality (MAPQ) in a BAM files
+Shows the data as a table and a barplot
+
+**Inputs**
+
+A bam alignment files which must be sorted
+
+**Output**
+
+A data frame of MAPQ counts
+
+A pdf barplot generated by R and ggplot2
+
+</help>
+
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+</citations>
+</tool>
+