# HG changeset patch
# User iuc
# Date 1680904826 0
# Node ID d1fad35bdb4a5d8ac788dc3862db4250ee7830a9
# Parent  95286af4139b21d9ee6d2f307b676a3b55af41ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

diff -r 95286af4139b -r d1fad35bdb4a macros.xml
--- a/macros.xml	Tue Mar 22 23:19:46 2022 +0000
+++ b/macros.xml	Fri Apr 07 22:00:26 2023 +0000
@@ -343,7 +343,7 @@
                 <option value="fixed">Fixed</option>
             </param>
             <when value="snp">
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -351,9 +351,9 @@
                 </param>
             </when>
             <when value="bounded">
-                <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
-                <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
+                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -373,7 +373,7 @@
                 <option value="fixed">Fixed</option>
             </param>
             <when value="snp">
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -381,9 +381,9 @@
                 </param>
             </when>
             <when value="bounded">
-                <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
-                <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
+                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -391,7 +391,7 @@
                 </param>
             </when>
             <when value="fixed">
-                <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
+                <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
             </when>
         </conditional>
     </xml>
diff -r 95286af4139b -r d1fad35bdb4a stacks_populations.xml
--- a/stacks_populations.xml	Tue Mar 22 23:19:46 2022 +0000
+++ b/stacks_populations.xml	Fri Apr 07 22:00:26 2023 +0000
@@ -1,9 +1,9 @@
-<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.2">
+<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.3">
     <description>analyze a population of individual samples ('populations' program)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -20,11 +20,11 @@
                     #set $filename = $filename + ".tsv"
                 #end if
                 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename)
-                    ln -s '${input_file}' 'stacks_outputs/${filename}' &&
+                    cp '${input_file}' 'stacks_outputs/${filename}' &&
                 #end if
             #end for
         #else if str($options_usage.input_type) == 'vcf'
-            ln -s '$options_usage.input_vcf' 'stacks_outputs/batch_1.vcf' &&
+            cp '$options_usage.input_vcf' 'stacks_outputs/batch_1.vcf' &&
         #end if
 
         populations
@@ -66,13 +66,13 @@
         ## Fstats
         $fstats
 
-        #if $options_kernel.kernel
+        #if $options_kernel.kernel != ""
             -k
             --sigma $options_kernel.sigma
         #end if
 
         ## Bootstrap resampling options
-        #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all
+        #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all != ""
             --bootstrap
         #else
             $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_pifis
@@ -107,7 +107,7 @@
         $populations_output.phylip_var_all
         $populations_output.treemix
 
-        #if $populations_output.options_genomic.genomic
+        #if $populations_output.options_genomic.genomic != ''
             --genomic
             -e $populations_output.options_genomic.enzyme
         #end if
@@ -151,7 +151,7 @@
             <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" />
             <param name="mindepth" argument="-m" type="integer" value="1" label="Specify a minimum stack depth required for individuals at a locus" />
             <param name="minminor" argument="--min_maf" type="float" value="0.25" label="Specify a minimum minor allele frequency required before calculating Fst at a locus (between 0 and 0.5)" />
-            <param name="max_obs_het" 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 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." />
 
             <conditional name="correction_select">
                 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'" >
@@ -174,66 +174,72 @@
 
             <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
 
-            <param name="write_single_snp" argument="--write_single_snp" truevalue="--write_single_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to only the first SNP per locus." />
-            <param name="write_random_snp" argument="--write_random_snp" truevalue="--write_random_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to one random SNP per locus." />
+            <param argument="--write_single_snp" truevalue="--write_single_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to only the first SNP per locus." />
+            <param argument="--write_random_snp" truevalue="--write_random_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to one random SNP per locus." />
         </section>
 
         <section name="populations_output" title="Output options" expanded="true">
-            <param name="ordered_export" 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 name="vcf" argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
-            <param name="vcf_haplotypes" argument="--vcf_haplotypes" truevalue="--vcf_haplotypes" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Variant Call Format (VCF)." />
-            <param name="genepop" argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" />
-            <param name="structure" argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" />
-            <param name="fasta" argument="--fasta" truevalue="--fasta" falsevalue="" type="boolean" checked="false" label="Output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility." />
-            <param name="fasta_strict" argument="--fasta_strict" truevalue="--fasta_strict" falsevalue="" type="boolean" checked="false" label="Output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci." />
-            <param name="hzar" argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." />
-            <param name="phase" argument="--phase" truevalue="--phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />
-            <param name="fastphase" argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" />
-            <param name="beagle" argument="--beagle" truevalue="--beagle" falsevalue="" type="boolean" checked="false" label="Output genotypes in Beagle format" />
-            <param name="beagle_phased" argument="--beagle_phased" truevalue="--beagle_phased" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Beagle format" />
-            <param name="plink" argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" />
-            <param name="phylip" 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 name="phylip_var" argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." />
-            <param name="phylip_var_all" 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 name="treemix" 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="--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="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
+            <param argument="--vcf_haplotypes" truevalue="--vcf_haplotypes" falsevalue="" type="boolean" checked="false" label="Output haplotypes 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="--fasta" truevalue="--fasta" falsevalue="" type="boolean" checked="false" label="Output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility." />
+            <param argument="--fasta_strict" truevalue="--fasta_strict" falsevalue="" type="boolean" checked="false" label="Output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci." />
+            <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) 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="--beagle" truevalue="--beagle" falsevalue="" type="boolean" checked="false" label="Output genotypes in Beagle format" />
+            <param argument="--beagle_phased" truevalue="--beagle_phased" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Beagle format" />
+            <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK 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)." />
 
             <conditional name="options_genomic">
-                <param name="genomic" argument="--genomic" truevalue="--genomic" falsevalue="" type="boolean" checked="false" label="Output each nucleotide position (fixed or polymorphic) in all population members to a file" />
+                <param argument="--genomic" type="select" checked="false" label="Output each nucleotide position (fixed or polymorphic) in all population members to a file">
+                    <option value="--genomic">Yes</option>
+                    <option value="">No</option>
+                </param>
                 <when value="--genomic">
                     <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
                         <expand macro="enzymes"/>
                     </param>
                 </when>
-                <when value="">
-                </when>
+                <when value=""/>
             </conditional>
         </section>
 
-        <param name="fstats" argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" />
+        <param argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" />
 
         <conditional name="options_kernel">
-            <param name="kernel" type="boolean" checked="false" truevalue="-k" falsevalue="" label="enable kernel-smoothed FIS, π, and FST calculations" />
+            <param name="kernel" type="select" checked="false" label="enable kernel-smoothed FIS, π, and FST calculations">
+                <option value="-k">Yes</option>
+                <option value="" selected="true">No</option>
+            </param>
             <when value="-k">
                 <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" />
             </when>
-            <when value="">
-            </when>
+            <when value=""/>
         </conditional>
 
         <section name="bootstrap_resampling" title="Bootstrap resampling" expanded="false">
             <conditional name="bootstrap_resampling_mode">
-                <param name="bootstrap_all" argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="Enable bootstrap resampling for all smoothed statistics" />
-                <when value="--bootstrap">
-                </when>
+                <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics">
+                    <option value="--bootstrap">Yes</option>
+                    <option value="" selected="true">No</option>
+                </param>
+                <when value="--bootstrap"/>
                 <when value="">
-                    <param name="bootstrap_pifis" argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" />
-                    <param name="bootstrap_fst" 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 name="bootstrap_div" 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 name="bootstrap_phist" 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 name="bootstrap_reps" argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />
-            <param name="bootstrap_wl" 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 -->