--- a/stacks_kmerfilter.xml	Wed Feb 27 09:50:00 2019 -0500
+++ b/stacks_kmerfilter.xml	Thu Jun 20 08:11:54 2019 -0400
@@ -45,6 +45,8 @@
 #if $options_kmer_char.k_dist
     | sed 's/KmerFrequency/# KmerFrequency/' > $kfreqdist
 #end if
+@TEE_APPEND_LOG@
+@CAT_LOG_TO_STDERR@
 
 ## move outputs such that Galaxy can find them
 ## if filtering is on then ...filt...fq is created
@@ -96,8 +98,10 @@
         <!--<section name="options_advanced_input" title="Advanced input options" expanded="False">
             <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="Read a set of kmers along with their frequencies of occurrence instead of reading raw input files" />
         </section>-->
+        <expand macro="in_log"/>
     </inputs>
     <outputs>
+        <expand macro="out_log"/>
         <data name="clean" format="fastqsanger" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
         </data>
@@ -124,6 +128,8 @@
                 <param name="input_type_select" value="single" />
                 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
             </conditional>
+            <param name="add_log" value="yes" />
+			<output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/>
             <param name="rare" value="--rare"/>
             <param name="abundant" value="--abundant" />
             <param name="k_len" value="16" />