--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pep_pointer.xml	Fri Dec 29 12:37:22 2017 -0500
@@ -0,0 +1,55 @@
+<tool id="pep_pointer" name="PepPointer" version="0.1.1">
+    <description>classify genomic location of peptides</description>
+    <requirements>
+        <requirement type="package" version="2.7.9">python</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
+    ]]></command>
+    <inputs>
+        <conditional name="gtf_input">
+            <param type="select" name="gtf_source" label="Choose the source of the GTF file">
+                <option value="cached" selected="true">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
+                    <options from_data_table="pep_pointer"/>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
+            </when>
+        </conditional>
+        <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gtf_source" value="history"/>
+            <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>