--- a/allele-counts.xml	Tue Aug 23 02:30:56 2016 -0400
+++ b/allele-counts.xml	Tue Mar 31 05:09:12 2020 -0400
@@ -1,6 +1,10 @@
-<tool id="allele_counts_1" version="1.2" name="Variant Annotator">
+<tool id="allele_counts_1" version="1.3" name="Variant Annotator">
   <description> process variant counts</description>
-  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+    <exit_code range=":-1" level="fatal" />
+  </stdio>
+  <command>allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt
   #if $seed:
     -r $seed
   #end if
@@ -15,12 +19,8 @@
     <param name="seed" type="text" value="" label="PRNG seed" />
   </inputs>
   <outputs>
-    <data name="output" format="tabular"/>
+    <data name="output" format="tabular" />
   </outputs>
-  <stdio>
-    <exit_code range="1:" err_level="fatal"/>
-    <exit_code range=":-1" err_level="fatal"/>
-  </stdio>
 
   <tests>
     <test>
@@ -114,4 +114,40 @@
 
   </help>
 
+  <citations>
+    <citation type="bibtex">
+      @article{Blankenberg2014,
+        author = {Blankenberg, Daniel and {Von Kuster}, Gregory and Bouvier, Emil and Baker, Dannon and Afgan, Enis and Stoler, Nicholas and Taylor, James and Nekrutenko, Anton},
+        doi = {10.1186/gb4161},
+        issn = {1465-6906},
+        journal = {Genome Biology},
+        keywords = {galaxy},
+        number = {2},
+        pages = {403},
+        title = {{Dissemination of scientific software with Galaxy ToolShed}},
+        url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb4161},
+        volume = {15},
+        year = {2014}
+      }
+    </citation>
+    <citation type="bibtex">
+      @article{Dickins2014,
+        archivePrefix = {arXiv},
+        arxivId = {15334406},
+        author = {Dickins, Benjamin and Rebolledo-Jaramillo, Boris and Su, Marcia Shu Wei and Paul, Ian M and Blankenberg, Daniel and Stoler, Nicholas and Makova, Kateryna D and Nekrutenko, Anton},
+        doi = {10.2144/000114146},
+        eprint = {15334406},
+        isbn = {5049880467},
+        issn = {19409818},
+        journal = {BioTechniques},
+        number = {3},
+        pages = {134--141},
+        pmid = {24641477},
+        title = {{Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach}},
+        volume = {56},
+        year = {2014}
+      }
+    </citation>
+  </citations>
+
 </tool>