--- a/umi-tools_extract.xml	Thu Aug 10 06:37:09 2017 -0400
+++ b/umi-tools_extract.xml	Tue Aug 29 17:37:07 2017 -0400
@@ -1,8 +1,9 @@
-<tool id="umi_tools_extract" name="UMI-tools extract" version="0.4.4.0">
+<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0">
     <description>Extract UMI from fastq files</description>
-    <requirements>
-        <requirement type="package" version="0.4.4">umi_tools</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         #set $gz = False
         #if $input_type.type == 'single':
@@ -150,16 +151,16 @@
             <param name="quality_filter_threshold" value="10" />
             <param name="quality_encoding" value="phred33" />
             <output name="out" file="out_SE.fastq" />
-            <output name="out_log" file="out_single.log" lines_diff="15"/>
+            <output name="out_log" file="out_single.log" lines_diff="22"/>
         </test>
         <test>
             <param name="type" value="paired" />
             <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
             <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
             <param name="bc_pattern" value="NNNXXX" />
-            <output name="out1" file="out_R1.fastq.gz" decompress="true" />
-            <output name="out2" file="out_R2.fastq.gz" decompress="true" />
-            <output name="out_log" file="out_paired.log" lines_diff="10"/>
+            <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
+            <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
+            <output name="out_log" file="out_paired.log" lines_diff="16"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -241,15 +242,5 @@
 and end two to FASTQOUT.
 
     ]]></help>
-    <citations>
-        <citation type="doi">10.1101/gr.209601.116</citation>
-        <citation type="bibtex">
-            @misc{githubUMI-tools,
-            title = {UMI-tools},
-            publisher = {GitHub},
-            journal = {GitHub repository},
-            url = {https://github.com/CGATOxford/UMI-tools},
-            }
-        </citation>
-    </citations>
+    <expand macro="citations" />
 </tool>