--- a/stacks_gstacks.xml	Mon Jul 01 10:59:14 2019 -0400
+++ b/stacks_gstacks.xml	Mon Sep 30 14:19:17 2019 -0400
@@ -11,6 +11,14 @@
 @FASTQ_INPUT_FUNCTIONS@
 
 mkdir bam_inputs stacks_outputs &&
+
+## annoyingly gstacks creates stacks_output/gstacks.log
+## instead of just writing to stderr as the other tools
+## hence we do not use the tokens and return populations.log as log file and take the stderr
+#if $output_log
+    ln -s '$output_log' stacks_outputs/gstacks.log &&
+#end if
+
 #if $mode_cond.mode_select == "denovo" and not $popmap:
     ## since collections have no len .. yet
     #try:
@@ -88,14 +96,6 @@
     #end if
 #end if
 
-
-## annoyingly gstacks creates stacks_output/gstacks.log
-## instead of just writing to stderr as the other tools
-## hence we do not use the tokens and return populations.log as log file and take the stderr
-#if $output_log
-    && mv stacks_outputs/gstacks.log $output_log
-#end if
-
 @EXTRACT_VCF@
 
 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
@@ -250,7 +250,6 @@
             <param name="add_log" value="yes" />
             <assert_command>
                 <has_text text="--ignore-pe-reads" />
-                <has_text text="--rm-pcr-duplicates" />
                 <has_text text="--kmer-length 23" />
                 <has_text text="--max-debruijn-reads 666" />
                 <has_text text="--min-kmer-cov 3" />
@@ -270,15 +269,15 @@
                 <param name="mode_select" value="refbased"/>
                 <conditional name="paired_cond">
                     <param name="paired_select" value=""/>
-                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
+                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails-->
                     <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
                 </conditional>
             </conditional>
             <param name="add_log" value="yes" />
             <assert_command>
-                <has_text text="-I bam_inputs" />
-                <not_has_text text="-B " />
-                <has_text text="--rm-unpaired-reads" />
+                <not_has_text text="-I bam_inputs" />
+                <has_text text="-B " />
+                <not_has_text text="--rm-unpaired-reads" />
                 <has_text text="--rm-pcr-duplicates" />
             </assert_command>
         </test>
@@ -296,7 +295,7 @@
                     <param name="min_mapq" value="23" />
                     <param name="max_clipped" value="0.23" />
                     <param name="max_insert_len" value="666" />
-                    <param name="details" value="--detailed"/>
+                    <param name="details" value="--details"/>
                     <param name="phasing_cooccurrences_thr_min" value="2"/>
                     <param name="phasing_cooccurrences_thr_max" value="3"/>
                     <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
@@ -307,13 +306,13 @@
             <param name="model_cond|var_alpha" value="0.1" />
             <param name="add_log" value="yes" />
             <assert_command>
-                <not_has_text text="-I bam_inputs" />
-                <has_text text="-B " />
+                <has_text text="-I bam_inputs" />
+                <not_has_text text="-B " />
                 <has_text text="--unpaired" />
                 <has_text text="--min-mapq 23" />
                 <has_text text="--max-clipped 0.23" />
                 <has_text text="--max-insert-len 666" />
-                <has_text text="--detailed" />
+                <has_text text="--details" />
                 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
                 <has_text text="--phasing-dont-prune-hets" />
                 <has_text text="--model snp" />
@@ -333,8 +332,8 @@
             </conditional>
             <param name="add_log" value="yes" />
             <assert_command>
-                <has_text text="-I bam_inputs" />
-                <not_has_text text="-B " />
+                <not_has_text text="-I bam_inputs" />
+                <has_text text="-B " />
                 <has_text text="--ignore-pe-reads" />
             </assert_command>
             <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>