--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfannotategenotypes.xml	Thu Mar 19 12:40:45 2015 -0400
@@ -0,0 +1,34 @@
+<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3">
+  <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
+    <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
+    <param name="tag_option" size="20" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+ <tests>
+    <test>
+      <param name="tag_option" value="added-genotypes"/>
+      <param name="input1" value="vcflib.vcf"/>
+      <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
+      <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
+    </test>
+    </tests>
+<help>
+
+Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation.  Also adds a 'has\_variant' flag for sites where the second file has a variant.
+
+-----
+
+Vcfannotate @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>