--- a/stacks_populations.xml	Wed Feb 12 18:22:03 2020 -0500
+++ b/stacks_populations.xml	Thu Jul 16 07:32:42 2020 -0400
@@ -51,14 +51,14 @@
 --min-samples-per-pop $options_filtering.minperc
 --min-samples-overall $options_filtering.min_samples_overall
 $options_filtering.filter_haplotype_wise
---min_maf $options_filtering.min_maf
---min_mac $options_filtering.min_mac
+--min-maf $options_filtering.min_maf
+--min-mac $options_filtering.min_mac
 #if str($options_filtering.max_obs_het)
-    --max_obs_het $options_filtering.max_obs_het
+    --max-obs-het $options_filtering.max_obs_het
 #end if
 ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
 ## #if str($options_filtering.lnl)
-##     --lnl_lim $options_filtering.lnl
+##     --lnl-lim $options_filtering.lnl
 ## #end if
 $options_filtering.filter_single_snp
 #if $options_filtering.blacklist
@@ -73,7 +73,7 @@
     -e $merge_phase.enzyme
 #end if
 $merge_phase.merge_sites
---merge_prune_lim $merge_phase.merge_prune_lim
+--merge-prune-lim $merge_phase.merge_prune_lim
 
 ## Locus stats:
 $locus_stats.hwe
@@ -81,9 +81,9 @@
 ## Fstats
 #if str($fstats_conditional.fstats) != 'no':
     --fstats
-    #if str( $fstats_conditional.correction_select.fst_correction ) != "no_corr"
-        --fst_correction $fstats_conditional.correction_select.fst_correction
-        --p_value_cutoff $fstats_conditional.correction_select.p_value_cutoff
+    $fstats_conditional.fst_correction
+    #if $fstats_conditional.fst_correction
+        --p-value-cutoff $fstats_conditional.p_value_cutoff
     #end if
 #end if
 
@@ -103,10 +103,10 @@
 
 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist:
     #if str($kernel_smoothing.bootstrap_reps)
-        --bootstrap_reps $kernel_smoothing.bootstrap_reps
+        --bootstrap-reps $kernel_smoothing.bootstrap_reps
     #end if
     #if $kernel_smoothing.bootstrap_wl
-        --bootstrap_wl '$kernel_smoothing.bootstrap_wl'
+        --bootstrap-wl '$kernel_smoothing.bootstrap_wl'
     #end if
 #end if
 
@@ -130,6 +130,13 @@
 $populations_output.no_hap_exports
 $populations_output.fasta_samples_raw
 
+#if $genetic_map_options.map_type:
+    --map-type $genetic_map_options.map_type
+#end if
+#if $genetic_map_options.map_format
+    --map-format $genetic_map_options.map_format
+#end if
+
 ## Additional options:
 
 $advanced_options.log_fst_comp
@@ -146,6 +153,12 @@
     #end if
     && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done
 #end if
+
+## move the genotype output (note that in 2.52 there is an inconsistent
+## naming for onemap output and also extensions are inconsistent -> therefore wildcard)
+#if $genetic_map_options.map_type and $genetic_map_options.map_format
+    && mv stacks_outputs/populations.${genetic_map_options.map_type}.* stacks_outputs/populations.sql.tsv
+#end if
     ]]></command>
 
     <inputs>
@@ -158,31 +171,31 @@
                 <expand macro="input_aln_macro"/>
             </when>
             <when value="vcf">
-                <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" />
+                <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V"/>
             </when>
         </conditional>
         <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" help="Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'." optional="true"/>
-        <param argument="--batch_size" type="integer" value="" optional="true" label="Number of loci to process in a batch"  help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/>
+        <param argument="--batch-size" type="integer" value="" optional="true" label="Number of loci to process in a batch"  help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/>
 
         <!-- Data Filtering -->
         <section name="options_filtering" title="Data filtering options" expanded="true">
 
-            <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" />
-            <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" />
-            <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus" />
-            <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data." />
-            <param argument="--min_maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" />
-            <param argument="--min_mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus" />
-            <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." />
+            <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population"/>
+            <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus"/>
+            <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus"/>
+            <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data."/>
+            <param argument="--min-maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus"/>
+            <param argument="--min-mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus"/>
+            <param argument="--max-obs-het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus."/>
             <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
-            <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold" />-->
+            <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold"/>-->
             <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" >
                 <option value="">yes</option>
-                <option value="--write_single_snp">No: Analyse only the first SNP (--write_single_snp)</option>
-                <option value="--write_random_snp">No: Analyse only one random SNP (--write_random_snp)</option>
+                <option value="--write-single-snp">No: Analyse only the first SNP (--write-single-snp)</option>
+                <option value="--write-random-snp">No: Analyse only one random SNP (--write-random-snp)</option>
             </param>
-            <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" />
-            <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" />
+            <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export"/>
+            <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export"/>
         </section>
 
         <!-- merging and Phasing -->
@@ -190,13 +203,13 @@
             <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
                 <expand macro="enzymes"/>
             </param>
-            <param argument="--merge_sites" truevalue="--merge_sites" falsevalue="" type="boolean" checked="false" label="Merge loci that were produced from the same restriction enzyme cutsite" help="(requires reference-aligned data)" />
-            <param argument="--merge_prune_lim" type="float" value="1.0" min="0.0" max="1.0" label="Fraction of samples possessing both loci to prune remaining samples from analysis" help="for merging adjacent loci"/>
+            <param argument="--merge-sites" truevalue="--merge-sites" falsevalue="" type="boolean" checked="false" label="Merge loci that were produced from the same restriction enzyme cutsite" help="(requires reference-aligned data)"/>
+            <param argument="--merge-prune-lim" type="float" value="1.0" min="0.0" max="1.0" label="Fraction of samples possessing both loci to prune remaining samples from analysis" help="for merging adjacent loci"/>
         </section>
 
         <!-- Locus stats -->
         <section name="locus_stats" title="Locus Stats" expanded="true">
-            <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus" />
+            <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus"/>
         </section>
 
         <!-- Fstats -->
@@ -207,46 +220,30 @@
             </param>
             <when value="no"/>
             <when value="yes">
-                <conditional name="correction_select">
-                    <param argument="--fst_correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values" >
-                        <option value="no_corr">No correction</option>
-                        <option value="p_value">p_value</option>
-                        <option value="bonferroni_win">bonferroni_win</option>
-                        <option value="bonferroni_gen">bonferroni_gen</option>
-                    </param>
-                    <when value="no_corr"/>
-                    <when value="p_value">
-                        <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
-                    </when>
-                    <when value="bonferroni_win">
-                        <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
-                    </when>
-                    <when value="bonferroni_gen">
-                        <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
-                    </when>
-                </conditional>
+                <param argument="--fst-correction" truevalue="--fst-correction" falsevalue="" type="boolean" checked="false" label="apply a p-value correction to Fst values based on a Fisher's exact test" help=""/>
+                <param argument="--p-value-cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default)."/>
             </when>
         </conditional>
 
         <!-- File output options -->
         <section name="populations_output" title="Output options" expanded="true">
-            <param argument="--ordered_export" truevalue="--ordered_export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site." />
-            <param argument="--fasta_loci" truevalue="--fasta_loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format" />
-            <param argument="--fasta_samples" truevalue="--fasta_samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format" />
-            <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
-            <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" />
-            <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" />
-            <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format" />
-            <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />-->
-            <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" />
-            <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" />
-            <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." />
-            <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction" />
-            <param argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." />
-            <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip_var_all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation." />-->
-            <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="--ordered-export" truevalue="--ordered-export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site."/>
+            <param argument="--fasta-loci" truevalue="--fasta-loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format"/>
+            <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/>
+            <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/>
+            <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
+            <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
+            <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
+            <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>-->
+            <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/>
+            <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
+            <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
+            <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
+            <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/>
+            <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>-->
+            <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"/>
         </section>
 
         <!-- Kernel-smoothing algorithm -->
@@ -255,18 +252,18 @@
                 <param name="kernel" type="select" label="Enable kernel-smoothed calculations" >
                     <option value="">No</option>
                     <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</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>
+                    <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>
                 <when value=""/>
                 <when value="-k">
-                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
+                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
                 </when>
-                <when value="--smooth_fstats">
-                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
+                <when value="--smooth-fstats">
+                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
                 </when>
-                <when value="--smooth_popstats">
-                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
+                <when value="--smooth-popstats">
+                    <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
                 </when>
             </conditional>
             <conditional name="bootstrap_resampling_mode">
@@ -277,19 +274,34 @@
                 <when value="--bootstrap">
                 </when>
                 <when value="">
-                    <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" />
-                    <param argument="--bootstrap_fst" type="boolean" checked="false" truevalue="--bootstrap_fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs" />
-                    <param argument="--bootstrap_div" type="boolean" checked="false" truevalue="--bootstrap_div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes" />
-                    <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." />
+                    <param argument="--bootstrap-pifis" type="boolean" checked="false" truevalue="--bootstrap-pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations"/>
+                    <param argument="--bootstrap-fst" type="boolean" checked="false" truevalue="--bootstrap-fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs"/>
+                    <param argument="--bootstrap-div" type="boolean" checked="false" truevalue="--bootstrap-div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes"/>
+                    <param argument="--bootstrap-phist" type="boolean" checked="false" truevalue="--bootstrap-phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes."/>
                 </when>
             </conditional>
-            <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />
-            <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" />
+            <param argument="--bootstrap-reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate"/>
+            <param argument="--bootstrap-wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist"/>
         </section>
 
         <!-- Output options -->
         <section name="advanced_options" title="Advanced options" expanded="False">
-            <param argument="--log_fst_comp" type="boolean" checked="false" truevalue="--log_fst_comp" falsevalue="" label="Log components of Fst/Phi_st calculations to a dataset" />
+            <param argument="--log-fst-comp" type="boolean" checked="false" truevalue="--log-fst-comp" falsevalue="" label="Log components of Fst/Phi_st calculations to a dataset"/>
+        </section>
+
+        <!-- Genetic map output options (population map must specify a genetic cross): -->
+        <section name="genetic_map_options" title="Genetic map output options (population map must specify a genetic cross)" help="works only if a population map specifying only two groupings: 'parent' and 'progeny'" expanded="false">
+            <param argument="--map-type" type="select" optional="true" label="genetic map type to write" help="needs to be selected to trigger the additional Genotyping markers output">
+                <option value="CP">CP</option>
+                <option value="DH">DH</option>
+                <option value="F2">F2</option>
+                <option value="BC1">BC1</option>
+            </param>
+            <param argument="--map-format" type="select" optional="true" label="mapping program format to write" help="needs to be selected to trigger the additional Genotyping markers output">
+                <option value="joinmap">joinmap</option>
+                <option value="onemap">onemap</option>
+                <option value="rqtl">rqtl</option>
+            </param>
         </section>
         <expand macro="in_log"/>
     </inputs>
@@ -297,57 +309,55 @@
         <expand macro="out_log"/>
         <expand macro="populations_output_full"/>
     </outputs>
-
     <tests>
         <!-- test w gstacks output as input and default options -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="batch_size" value="9999" />
-            <param name="add_log" value="yes" />
+            <param name="batch_size" value="9999"/>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="batch_size" value="9999"/>
+            <param name="add_log" value="yes"/>
             <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
             <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
             <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
             <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
             <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
             <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
-            <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
         </test>
         <!-- test w gstacks output as input, wo popmap, and default options -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <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="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_sql"><assert_contents><has_text text="" /></assert_contents></output>
+            <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="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>
         </test>
         <!-- test w gstacks output as input and + all outputs -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="26">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="add_log" value="yes" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="add_log" value="yes"/>
             <param name="advanced_options|log_fst_comp" value="yes"/>
             <param name="fstats_conditional|fstats" value="yes"/>
             <param name="populations_output|fasta_loci" value="yes"/>
@@ -363,21 +373,20 @@
             <param name="populations_output|radpainter" value="yes"/>
             <param name="populations_output|treemix" value="yes"/>
             <assert_command>
-                <has_text text="--log_fst_comp" />
+                <has_text text="--log-fst-comp"/>
             </assert_command>
-            <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="Populations is done."/></assert_contents></output>
             <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
             <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
             <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
             <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
             <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
-            <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
 
             <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"/>
-			<output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
-			<output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " -->
+            <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
+            <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " -->
             <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/>
@@ -395,175 +404,207 @@
             <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
         </test>
         <!-- test w vcf input and default options, just checking if finished -->
-        <test>
-            <param name="options_usage|input_type" value="vcf" />
+        <test expect_num_outputs="6">
+            <param name="options_usage|input_type" value="vcf"/>
             <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
-            <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="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_sql"><assert_contents><has_text text="" /></assert_contents></output>
+            <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="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>
         </test>
         <!-- test w gstacks output as input and non default filtering -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="add_log" value="yes" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="add_log" value="yes"/>
             <section name="options_filtering">
                 <param name="minperc" value="0.1"/>
                 <param name="minpop" value="2"/>
                 <param name="min_samples_overall" value="0.01"/>
                 <param name="filter_haplotype_wise" value="--filter-haplotype-wise"/>
-                <param name="min_maf" value="0.01" />
+                <param name="min_maf" value="0.01"/>
                 <param name="min_mac" value="1"/>
-                <param name="max_obs_het" value="0.8" />
-                <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" />
+                <param name="max_obs_het" value="0.8"/>
+                <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
             </section>
             <assert_command>
-                <has_text text="--min-samples-per-pop 0.1" />
-                <has_text text="--min-populations 2" />
-                <has_text text="--min-samples-overall 0.01" />
-                <has_text text="--filter-haplotype-wise" />
-                <has_text text="--min_maf 0.01" />
-                <has_text text="--min_mac 1" />
-                <has_text text="--max_obs_het 0.8" />
-                <has_text text="-B " />
+                <has_text text="--min-samples-per-pop 0.1"/>
+                <has_text text="--min-populations 2"/>
+                <has_text text="--min-samples-overall 0.01"/>
+                <has_text text="--filter-haplotype-wise"/>
+                <has_text text="--min-maf 0.01"/>
+                <has_text text="--min-mac 1"/>
+                <has_text text="--max-obs-het 0.8"/>
+                <has_text text="-B "/>
             </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_sql"><assert_contents><has_text text="" /></assert_contents></output>
+            <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>
         </test>
         <!-- test w gstacks output as input and non default filtering (needed because filter-haplotype-wise is incompatible with write_random_snp/write_single_snp) -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="add_log" value="yes" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="add_log" value="yes"/>
             <section name="options_filtering">
                 <param name="minperc" value="0.1"/>
                 <param name="minpop" value="2"/>
                 <param name="min_samples_overall" value="0.01"/>
-                <param name="min_maf" value="0.01" />
+                <param name="min_maf" value="0.01"/>
                 <param name="min_mac" value="1"/>
-                <param name="max_obs_het" value="0.8" />
+                <param name="max_obs_het" value="0.8"/>
                 <!-- since write_random_snp runs in infinite loop switch to write_single -->
-                <param name="filter_single_snp" value="--write_single_snp"/>
-                <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" />
+                <param name="filter_single_snp" value="--write-single-snp"/>
+                <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
             </section>
             <assert_command>
-                <has_text text="--min-samples-per-pop 0.1" />
-                <has_text text="--min-populations 2" />
-                <has_text text="--min-samples-overall 0.01" />
-                <has_text text="--min_maf 0.01" />
-                <has_text text="--min_mac 1" />
-                <has_text text="--max_obs_het 0.8" />
-                <not_has_text text="--write_random_snp" />
-                <has_text text="-B " />
+                <has_text text="--min-samples-per-pop 0.1"/>
+                <has_text text="--min-populations 2"/>
+                <has_text text="--min-samples-overall 0.01"/>
+                <has_text text="--min-maf 0.01"/>
+                <has_text text="--min-mac 1"/>
+                <has_text text="--max-obs-het 0.8"/>
+                <not_has_text text="--write-random-snp"/>
+                <has_text text="-B "/>
             </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_sql"><assert_contents><has_text text="" /></assert_contents></output>
+            <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>
         </test>
         <!-- test w gstacks output as input and non default merging/hwe -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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="gstacks/catalog.calls.vcf" />
-                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <section name="merge_phase">
                 <param name="enzyme" value="ecoRI"/>
                 <param name="merge_sites" value="yes"/>
-                <param name="merge_prune_lim" value="0.9" />
+                <param name="merge_prune_lim" value="0.9"/>
             </section>
             <section name="locus_stats">
-                <param name="hwe" value="yes" />
+                <param name="hwe" value="yes"/>
             </section>
-            <param name="add_log" value="yes" />
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <has_text text="-e ecoRI" />
-                <has_text text="--merge_sites" />
-                <has_text text="--merge_prune_lim 0.9" />
-                <has_text text="--hwe" />
+                <has_text text="-e ecoRI"/>
+                <has_text text="--merge-sites"/>
+                <has_text text="--merge-prune-lim 0.9"/>
+                <has_text text="--hwe"/>
             </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_sql"><assert_contents><has_text text="" /></assert_contents></output>
-            <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="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>
         </test>
         <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
-        <test>
-            <param name="options_usage|input_type" value="stacks" />
+        <test expect_num_outputs="6">
+            <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" />
+                    <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" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <conditional name="fstats_conditional">
-                <param name="fstats" value="yes" />
-                <conditional name="correction_select">
-                    <param name="fst_correction" value="bonferroni_gen"/>
-                    <param name="p_value_cutoff" value="0.01" />
-                </conditional>
+                <param name="fstats" value="yes"/>
+                <param name="fst_correction" value="--fst-correction"/>
+                <param name="p_value_cutoff" value="0.01"/>
             </conditional>
             <conditional name="options_kernel">
-                <param name="kernel" value="-k" />
-                <param name="sigma" value="150001" />
+                <param name="kernel" value="-k"/>
+                <param name="sigma" value="150001"/>
             </conditional>
             <conditional name="bootstrap_resampling_mode">
-                <param name="bootstrap" value="--bootstrap" />
+                <param name="bootstrap" value="--bootstrap"/>
             </conditional>
-            <param name="bootstrap_reps" value="23" />
-            <param name="add_log" value="yes" />
+            <param name="bootstrap_reps" value="23"/>
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <has_text text="--fstats" />
-                <has_text text="--fst_correction bonferroni_gen" />
-                <has_text text="--p_value_cutoff 0.01" />
-                <has_text text="-k " />
-                <has_text text="--sigma 150001" />
-                <has_text text="--bootstrap" />
-                <has_text text="--bootstrap_reps 23" />
+                <has_text text="--fstats"/>
+                <has_text text="--fst-correction"/>
+                <has_text text="--p-value-cutoff 0.01"/>
+                <has_text text="-k "/>
+                <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="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_sql"><assert_contents><has_text text="" /></assert_contents></output>
+            <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>
+        </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">
+                <collection type="list">
+                    <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
+               </collection>
+            </param>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="add_log" value="yes"/>
+            <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
+            <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
+            <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
+            <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
+            <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
+            <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
+        </test>
+        <!-- test w gstacks output as input, wo popmap, and Genetic map output options that have been added in 2.5 -->
+        <test expect_num_outputs="7">
+            <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="gstacks/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
+               </collection>
+            </param>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/>
+            <section name="genetic_map_options">
+                <param name="map_type" value="CP"/>
+                <param name="map_format" value="joinmap"/>
+            </section>
+            <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="out_sql" file="populations/populations.CP.joinmap.loc" lines_diff="4"/>
+            <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>
         </test>
     </tests>
     <help>
@@ -625,5 +666,5 @@
 @STACKS_INFOS@
 ]]>
     </help>
-    <expand macro="citation" />
+    <expand macro="citation"/>
 </tool>