# HG changeset patch
# User matthias
# Date 1543511778 18000
# Node ID a8d93e132d3b0f69c83ee68925f0f329b2f103d0
# Parent  bd0bf17caa4d9cff964926669639af418349fd54
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

diff -r bd0bf17caa4d -r a8d93e132d3b stacks_refmap.xml
--- a/stacks_refmap.xml	Thu Nov 29 11:38:05 2018 -0500
+++ b/stacks_refmap.xml	Thu Nov 29 12:16:18 2018 -0500
@@ -20,6 +20,8 @@
 -T \${GALAXY_SLOTS:-1}
 --var-alpha $model_options.var_alpha
 --gt-alpha $model_options.gt_alpha
+
+&& mv stacks_outputs/ref_map.log $output_log
     ]]></command>
 
     <inputs>
@@ -52,7 +54,7 @@
             </param>
             <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
             <param name="add_log" value="yes" />
-            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
             <!-- TODO test for outputs -->
         </test>
         <test>
@@ -68,7 +70,7 @@
                 <has_text text="--gt-alpha 0.1" />
             </assert_command>
             <param name="add_log" value="yes" />
-            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
         </test>
     </tests>