--- a/stacks_populations.xml	Mon Jul 01 11:01:14 2019 -0400
+++ b/stacks_populations.xml	Mon Sep 30 14:17:47 2019 -0400
@@ -8,9 +8,11 @@
     <command detect_errors="aggressive"><![CDATA[
 #import re
 
-mkdir stacks_inputs stacks_outputs
+mkdir stacks_inputs stacks_outputs &&
 
-&&
+#if $output_log
+    ln -s '$output_log' stacks_outputs/populations.log &&
+#end if
 
 #if str($options_usage.input_type) == 'stacks'
     #for $input_file in $options_usage.input_aln
@@ -45,9 +47,9 @@
 
 ## Data filtering
 
--p $options_filtering.minpop
--r $options_filtering.minperc
--R $options_filtering.min_samples_overall
+--min-populations $options_filtering.minpop
+--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
@@ -143,10 +145,6 @@
         > $output_log
     #end if
     && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done
-#else
-    #if $output_log
-        && mv stacks_outputs/populations.log $output_log
-    #end if
 #end if
     ]]></command>
 
@@ -169,8 +167,8 @@
         <!-- Data Filtering -->
         <section name="options_filtering" title="Data filtering options" expanded="true">
 
-            <param name="minperc" argument="-r" 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="-p" type="integer" value="1" label="Minimum number of populations a locus must be present in to process 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" />
@@ -431,8 +429,8 @@
                 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" />
             </section>
             <assert_command>
-                <has_text text="-r 0.1" />
-                <has_text text="-p 2" />
+                <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" />
@@ -466,18 +464,18 @@
                 <param name="min_maf" value="0.01" />
                 <param name="min_mac" value="1"/>
                 <param name="max_obs_het" value="0.8" />
-                <!-- since write_random_snp runs in ifinite loop switch to write_single -->
+                <!-- 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" />
             </section>
             <assert_command>
-                <has_text text="-r 0.1" />
-                <has_text text="-p 2" />
+                <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" />
-                <has_text text="--write_random_snp" />
+                <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>