--- a/stacks_populations.xml	Thu Jul 16 07:32:42 2020 -0400
+++ b/stacks_populations.xml	Tue Apr 27 09:38:08 2021 +0000
@@ -129,6 +129,7 @@
 $populations_output.treemix
 $populations_output.no_hap_exports
 $populations_output.fasta_samples_raw
+$populations_output.gtf
 
 #if $genetic_map_options.map_type:
     --map-type $genetic_map_options.map_type
@@ -244,14 +245,15 @@
             <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/>
             <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/>
             <param argument="--fasta-samples-raw" truevalue="--fasta-samples-raw" falsevalue="" type="boolean" checked="false" label="Output all haplotypes observed in each sample, for each locus, in FASTA format"/>
+            <param argument="--gtf" truevalue="--gtf" falsevalue="" type="boolean" checked="false" label="output locus positions in a GTF annotation file"/>
         </section>
 
         <!-- Kernel-smoothing algorithm -->
         <section name="kernel_smoothing" title="Kernel smoothing" expanded="false">
             <conditional name="options_kernel">
-                <param name="kernel" type="select" label="Enable kernel-smoothed calculations" >
+                <param name="kernel" type="select" label="Enable kernel-smoothed calculations" help="The options -k and --smooth-fstats implicitly enable --fstats. Note that, in order to set non-default values for --fst-correction or --p-value-cutoff the option --fstats still needs to be enabled in the tool form." >
                     <option value="">No</option>
-                    <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option>
+                    <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k/--smooth)</option>
                     <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option>
                     <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option>
                 </param>
@@ -348,7 +350,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and + all outputs -->
-        <test expect_num_outputs="26">
+        <test expect_num_outputs="27">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -372,6 +374,7 @@
             <param name="populations_output|structure" value="yes"/>
             <param name="populations_output|radpainter" value="yes"/>
             <param name="populations_output|treemix" value="yes"/>
+            <param name="populations_output|gtf" value="yes"/>
             <assert_command>
                 <has_text text="--log-fst-comp"/>
             </assert_command>
@@ -402,6 +405,7 @@
             <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
+            <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " -->
         </test>
         <!-- test w vcf input and default options, just checking if finished -->
         <test expect_num_outputs="6">
@@ -526,7 +530,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -564,8 +568,54 @@
             <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
+            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
+            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
         </test>
-         <!-- test w gstacks output as input and default options -->
+        <!-- same as previous test but without fstats parameter in order to check if the filter 
+             for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats
+             is used) -->
+        <test expect_num_outputs="9">
+            <param name="options_usage|input_type" value="stacks"/>
+            <param name="options_usage|input_aln">
+                <collection type="list">
+                    <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
+               </collection>
+            </param>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <conditional name="fstats_conditional">
+                <param name="fstats" value="no"/>
+            </conditional>
+            <conditional name="options_kernel">
+                <param name="kernel" value="--smooth-fstats"/>
+                <param name="sigma" value="150001"/>
+            </conditional>
+            <conditional name="bootstrap_resampling_mode">
+                <param name="bootstrap" value="--bootstrap"/>
+            </conditional>
+            <param name="bootstrap_reps" value="23"/>
+            <param name="add_log" value="yes"/>
+            <assert_command>
+                <not_has_text text="--fstats"/>
+                <not_has_text text="--fst-correction"/>
+                <not_has_text text="--p-value-cutoff 0.01"/>
+                <has_text text="--smooth-fstats "/>
+                <has_text text="--sigma 150001"/>
+                <has_text text="--bootstrap"/>
+                <has_text text="--bootstrap-reps 23"/>
+            </assert_command>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
+            <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
+            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
+            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
+        </test>
+        <!-- test w gstacks output as input and default options -->
         <test expect_num_outputs="6">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">