--- a/stacks_clonefilter.xml	Wed Feb 27 10:03:16 2019 -0500
+++ b/stacks_clonefilter.xml	Thu Jun 20 08:18:09 2019 -0400
@@ -36,6 +36,8 @@
 ## only supports fastq.gz output since the
 ## the program outputs empty files for fasta/fastq
 -y gzfastq
+@TEE_APPEND_LOG@
+@CAT_LOG_TO_STDERR@
 
 ## move outputs such that Galaxy can find them
 #if $capture:
@@ -59,8 +61,10 @@
         <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
         <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
         <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" />
+        <expand macro="in_log"/>
     </inputs>
     <outputs>
+        <expand macro="out_log"/>
         <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'single'</filter>
         </data>
@@ -82,6 +86,8 @@
                 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
             </conditional>
             <param name="oligo_len_1" value="6" />
+            <param name="add_log" value="yes" />
+			<output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
             <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
         </test>
         <!-- single end, alt BCencoding, capture-->