--- a/flash.xml	Thu Oct 19 17:32:41 2017 -0400
+++ b/flash.xml	Wed Nov 08 11:06:11 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="flash" name="FLASH" version="@VERSION@.2">
+<tool id="flash" name="FLASH" version="@VERSION@.3">
     <description>adjust length of short reads</description>
     <macros>
         <token name="@VERSION@">1.2.11</token>
@@ -27,6 +27,10 @@
                 #else:
                     -p 64
                 #end if
+
+                #if $save_log:
+                    > '$log'
+                #end if
         ]]>
     </command>
     <inputs>
@@ -48,6 +52,7 @@
         <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
         <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
         <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
+        <param name="save_log" type="boolean" truevalue="" falsevalue="" checked="false" label="Save FLASH log file" />
     </inputs>
     <outputs>
         <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
@@ -69,6 +74,9 @@
             <filter>layout['select_layout'] == 'individual'</filter>
         </data>
         <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
+        <data format="txt" name="log" label="${tool.name} on ${on_string}: Raw Log">
+          <filter>raw_log == 'yes'</filter>
+        </data>
         <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
             <filter>generate_histogram</filter>
         </data>
@@ -91,10 +99,16 @@
             <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
             <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
             <param name="generate_histogram" value="false" />
+            <param name="save_log" value="true" />
             <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
             <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
             <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
             <output name="hist" file="flash_hist_out1.tabular" />
+            <output name="log">
+              <assert_contents>
+                <has_line_matching expression=".*Percent combined: 3.60%" />
+              </assert_contents>
+            </output>
         </test>
         <test>
             <param name="select_layout" value="individual" />
@@ -102,6 +116,7 @@
             <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
             <param name="allow_outies" value="true" />
             <param name="generate_histogram" value="true" />
+            <param name="save_log" value="true" />            
             <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
             <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
             <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
@@ -111,6 +126,11 @@
             <output name="histogram_in" file="flash_hist_in_out2.txt" />
             <output name="hist_out" file="flash_hist_out_out2.tabular" />
             <output name="histogram_out" file="flash_hist_out_out2.txt" />
+            <output name="log">
+              <assert_contents>
+                <has_line_matching expression=".*Percent combined: 3.80%" />
+              </assert_contents>
+            </output>
         </test>
         <test>
             <param name="select_layout" value="collection" />