--- a/stacks_gstacks.xml	Tue Apr 27 09:18:07 2021 +0000
+++ b/stacks_gstacks.xml	Wed Sep 01 11:16:14 2021 +0000
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="1.13">samtools</requirement>
     </expand>
     <expand macro="version_cmd"/>
     <command detect_errors="aggressive"><![CDATA[
@@ -88,11 +88,11 @@
 ## exit codes and stderr output) this adds the samtools requirement
 ## for later versions where this is fixed the output bam files could just be moved
 ## to stacks_outputs if this is still necessary
-#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != ""
+#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments
     #if $popmap:
-        && for b in stacks_outputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
+        && for b in stacks_outputs/*alns.bam; do (samtools view --no-PG -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
     #else
-        && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
+        && (samtools view --no-PG -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
     #end if
 #end if
 
@@ -117,17 +117,17 @@
                 <option value="refbased">Reference-based</option>
             </param>
             <when value="denovo">
-                <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
+                <param argument="--ignore-pe-reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
                 <conditional name="advanced_cond">
                     <param name="advanced_select" type="select" label="Advanced options">
                         <option value="no">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
-                        <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
-                        <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
-                        <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
+                        <param argument="--kmer-length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
+                        <param argument="--max-debruijn-reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
+                        <param argument="--min-kmer-cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
+                        <param argument="--write-alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -140,8 +140,8 @@
                         <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
                     </param>
                     <when value="">
-                        <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
-                        <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
+                        <param argument="--rm-unpaired-reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
+                        <param argument="--rm-pcr-duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
                     </when>
                     <when value="--unpaired"/>
                     <when value="--ignore-pe-reads"/>
@@ -152,13 +152,13 @@
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
-                        <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
-                        <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
+                        <param argument="--min-mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
+                        <param argument="--max-clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
+                        <param argument="--max-insert-len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
                         <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/>
                         <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/>
                         <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>
-                        <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
+                        <param argument="--phasing-dont-prune-hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -203,7 +203,7 @@
             <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/>
             <output_collection name="gstacks_out" type="list" count="2">
                 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
-                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>
+                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" decompress="true" compare="diff"/>
             </output_collection>
         </test>
         <!-- denovomode, w popmap, write alignments -->
@@ -214,7 +214,7 @@
                 <param name="mode_select" value="denovo"/>
                 <conditional name="advanced_cond">
                     <param name="advanced_select" value="yes"/>
-                    <param name="write_alignments" value="--write-alignments"/>
+                    <param name="write_alignments" value="true"/>
                 </conditional>
             </conditional>
             <param name="add_log" value="yes"/>