--- a/peakachu.xml	Thu Feb 15 15:59:41 2018 -0500
+++ b/peakachu.xml	Tue May 22 11:47:18 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="peakachu" name="PEAKachu" version="0.1.0.0">
+<tool id="peakachu" name="PEAKachu" version="0.1.0.1">
     <description>Calls Peaks in CLIP data</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
@@ -65,10 +65,18 @@
         --padj_threshold $padj_threshold
 
         &&
-        head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
-        tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
-        mv peaks.tsv '$peak_tables' &&
-        mv ./tmp_output/plots/Initial*.png '$MA_plot'
+        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
+        then 
+            head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
+            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
+            mv peaks.tsv '$peak_tables' &&
+            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
+            mv peak_annotations.gff '$peak_annotations' &&
+            mv ./tmp_output/plots/Initial*.png '$MA_plot';
+        else 
+            echo "No Peaks Found" >&2;
+        fi 
+
 
     ]]>
     </command>
@@ -157,6 +165,7 @@
     </inputs>
     <outputs>
         <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/>
+        <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/>
         <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
     </outputs>
     <tests>
@@ -164,7 +173,7 @@
             <param name="experimentLibs" value="test1_+xl.bam"/>
             <param name="controlLibs" value="test1_-xl.bam"/>
             <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
-            <output name="MA_plot" ftype="png" file="test1_MA.png"/>
+            <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
         </test>
     </tests>
     <help>