# HG changeset patch
# User kevyin
# Date 1351825553 14400
# Node ID 1bce61936d450ab2b50f5b233c7b6268aa54f631
# Parent  31b95602305dc088d54ee816e9f978c450a9aba2
Uploaded

diff -r 31b95602305d -r 1bce61936d45 annotatePeaks.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotatePeaks.xml	Thu Nov 01 23:05:53 2012 -0400
@@ -0,0 +1,41 @@
+<tool id="homer-annotate-peaks" name="annotate-peaks" version="0.0.1">
+    <requirements>
+        <requirement type="package">homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
+        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular,bed" name="input_bed" type="data" label="Intervals in BED format" />
+        <param name="genome_selector" type="select" label="Genome version">
+            <option value="hg19" selected="true">hg19</option>
+        </param>
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="csv" name="out_annotated" label="Annotated" />
+        <data format="txt" name="out_log" label="homer_annotatePeaks.log" />
+    </outputs>
+    <tests>
+        <test>
+            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
+            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
+        </test>
+    </tests>
+
+    <help>
+
+        .. class:: infomark
+
+        **Homer annoatePeaks**
+        More information on accepted formats
+        http://biowhat.ucsd.edu/homer/ngs/annotation.html
+
+
+    </help>
+</tool>
+