--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pep_pointer.xml	Fri Dec 22 04:33:12 2017 -0500
@@ -0,0 +1,36 @@
+<tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="2.7.9">python</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified'
+    ]]></command>
+    <inputs>
+        <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
+        <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="classified"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gtf" value="mus17.gtf"/>
+            <param name="bed" value="novel_peptides_17.bed"/>
+            <output name="classified" file="classified_novel_peptides.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **PepPointer**
+
+        Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene. 
+    ]]></help>
+    <citations>
+      <citation type="bibtex">
+@misc{peppointer,
+    author={Kumar, Praveen},
+    year={2017},
+    title={PepPointer}
+}
+      </citation>
+    </citations>
+</tool>