--- a/stacks_gstacks.xml	Mon Sep 30 14:19:17 2019 -0400
+++ b/stacks_gstacks.xml	Wed Jul 15 17:24:38 2020 -0400
@@ -90,9 +90,9 @@
 ## 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 $popmap:
-        && for b in bam_inputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > stacks_outputs/\$(basename "\$b"); done
+        && for b in stacks_outputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
     #else
-        && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam
+        && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
     #end if
 #end if
 
@@ -109,7 +109,7 @@
 
     <inputs>
         <expand macro="bam_input_macro"/>
-        <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
+        <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/>
 
         <conditional name="mode_cond">
             <param name="mode_select" type="select" label="Mode">
@@ -117,16 +117,16 @@
                 <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" 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"/>
                 <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="--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"/>
                     </when>
                     <when value="no"/>
@@ -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" 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"/>
                     </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="--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 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="--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" 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"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -181,7 +181,7 @@
                 <expand macro="variant_calling_options_vg"/>
             </when>
         </conditional>
-        <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset" />
+        <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset"/>
         <expand macro="in_log"/>
     </inputs>
     <outputs>
@@ -193,74 +193,74 @@
         <!-- denovomode, w popmap -->
         <test expect_num_outputs="3">
             <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <conditional name="mode_cond">
                 <param name="mode_select" value="denovo"/>
             </conditional>
-            <param name="add_log" value="yes" />
-            <param name="add_log_distribs" value="yes" />
+            <param name="add_log" value="yes"/>
+            <param name="add_log_distribs" value="yes"/>
             <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
-            <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/>
+            <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="2"/>
-                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/>
+                <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="sim_size" delta_frac="0.01"/>
             </output_collection>
         </test>
         <!-- denovomode, w popmap, write alignments -->
         <test expect_num_outputs="3">
             <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <conditional name="mode_cond">
                 <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="--write-alignments"/>
                 </conditional>
             </conditional>
-            <param name="add_log" value="yes" />
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <has_text text="--write-alignments" />
+                <has_text text="--write-alignments"/>
             </assert_command>
-            <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
+            <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2"/>
             <output_collection name="gstacks_alns_out" type="list" count="2">
-                <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam" />
-                <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam" />
+                <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam"/>
+                <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam"/>
             </output_collection>
         </test>
         <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
         <test expect_num_outputs="3">
             <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
             <conditional name="mode_cond">
-                <param name="mode_select" value="denovo" />
-                <param name="ignore_pe_reads" value="--ignore-pe-reads" />
+                <param name="mode_select" value="denovo"/>
+                <param name="ignore_pe_reads" value="--ignore-pe-reads"/>
                 <conditional name="advanced_cond">
                     <param name="advanced_select" value="yes"/>
-                    <param name="kmer_length" value="23" />
+                    <param name="kmer_length" value="23"/>
                     <param name="max_debruijn_reads" value="666"/>
-                    <param name="min_kmer_cov" value="3" />
-                    <param name="write_alignments" value="--write-alignments" />
+                    <param name="min_kmer_cov" value="3"/>
+                    <param name="write_alignments" value="--write-alignments"/>
                 </conditional>
             </conditional>
             <conditional name="model_cond">
                 <param name="model" value="marukihigh"/>
-                <param name="var_alpha" value="0.1" />
-                <param name="gt_alpha" value="0.1" />
+                <param name="var_alpha" value="0.1"/>
+                <param name="gt_alpha" value="0.1"/>
             </conditional>
-            <param name="add_log" value="yes" />
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <has_text text="--ignore-pe-reads" />
-                <has_text text="--kmer-length 23" />
-                <has_text text="--max-debruijn-reads 666" />
-                <has_text text="--min-kmer-cov 3" />
-                <has_text text="--write-alignments" />
-                <has_text text="--model marukihigh" />
-                <has_text text="--var-alpha 0.1" />
-                <has_text text="--gt-alpha 0.1" />
+                <has_text text="--ignore-pe-reads"/>
+                <has_text text="--kmer-length 23"/>
+                <has_text text="--max-debruijn-reads 666"/>
+                <has_text text="--min-kmer-cov 3"/>
+                <has_text text="--write-alignments"/>
+                <has_text text="--model marukihigh"/>
+                <has_text text="--var-alpha 0.1"/>
+                <has_text text="--gt-alpha 0.1"/>
             </assert_command>
-            <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
+            <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2"/>
-            <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam" />
+            <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam"/>
         </test>
         <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
         <test expect_failure="true" expect_exit_code="1">
@@ -269,56 +269,56 @@
                 <param name="mode_select" value="refbased"/>
                 <conditional name="paired_cond">
                     <param name="paired_select" value=""/>
-                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails-->
-                    <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
+                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads"/> removes too much of the test data and gstacks fails-->
+                    <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
                 </conditional>
             </conditional>
-            <param name="add_log" value="yes" />
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <not_has_text text="-I bam_inputs" />
-                <has_text text="-B " />
-                <not_has_text text="--rm-unpaired-reads" />
-                <has_text text="--rm-pcr-duplicates" />
+                <not_has_text text="-I bam_inputs"/>
+                <has_text text="-B "/>
+                <not_has_text text="--rm-unpaired-reads"/>
+                <has_text text="--rm-pcr-duplicates"/>
             </assert_command>
         </test>
         <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
         <test expect_num_outputs="2">
             <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <conditional name="mode_cond">
                 <param name="mode_select" value="refbased"/>
                 <conditional name="paired_cond">
                     <param name="paired_select" value="--unpaired"/>
                 </conditional>
                 <conditional name="advanced_cond">
-                    <param name="advanced_select" value="yes" />
-                    <param name="min_mapq" value="23" />
-                    <param name="max_clipped" value="0.23" />
-                    <param name="max_insert_len" value="666" />
+                    <param name="advanced_select" value="yes"/>
+                    <param name="min_mapq" value="23"/>
+                    <param name="max_clipped" value="0.23"/>
+                    <param name="max_insert_len" value="666"/>
                     <param name="details" value="--details"/>
                     <param name="phasing_cooccurrences_thr_min" value="2"/>
                     <param name="phasing_cooccurrences_thr_max" value="3"/>
-                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
+                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets"/>
                 </conditional>
             </conditional>
             <param name="model_cond|model" value="snp"/>
-            <param name="model_cond|gt_alpha" value="0.1" />
-            <param name="model_cond|var_alpha" value="0.1" />
-            <param name="add_log" value="yes" />
+            <param name="model_cond|gt_alpha" value="0.1"/>
+            <param name="model_cond|var_alpha" value="0.1"/>
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <has_text text="-I bam_inputs" />
-                <not_has_text text="-B " />
-                <has_text text="--unpaired" />
-                <has_text text="--min-mapq 23" />
-                <has_text text="--max-clipped 0.23" />
-                <has_text text="--max-insert-len 666" />
-                <has_text text="--details" />
-                <has_text text="--phasing-cooccurrences-thr-range 2,3" />
-                <has_text text="--phasing-dont-prune-hets" />
-                <has_text text="--model snp" />
-                <has_text text="--gt-alpha 0.1" />
+                <has_text text="-I bam_inputs"/>
+                <not_has_text text="-B "/>
+                <has_text text="--unpaired"/>
+                <has_text text="--min-mapq 23"/>
+                <has_text text="--max-clipped 0.23"/>
+                <has_text text="--max-insert-len 666"/>
+                <has_text text="--details"/>
+                <has_text text="--phasing-cooccurrences-thr-range 2,3"/>
+                <has_text text="--phasing-dont-prune-hets"/>
+                <has_text text="--model snp"/>
+                <has_text text="--gt-alpha 0.1"/>
             </assert_command>
-            <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
+            <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2"/>
         </test>
         <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
@@ -330,13 +330,13 @@
                     <param name="paired_select" value="--ignore-pe-reads"/>
                 </conditional>
             </conditional>
-            <param name="add_log" value="yes" />
+            <param name="add_log" value="yes"/>
             <assert_command>
-                <not_has_text text="-I bam_inputs" />
-                <has_text text="-B " />
-                <has_text text="--ignore-pe-reads" />
+                <not_has_text text="-I bam_inputs"/>
+                <has_text text="-B "/>
+                <has_text text="--ignore-pe-reads"/>
             </assert_command>
-            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
+            <output name="output_log"><assert_contents><has_text text="gstacks is done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2"/>
         </test>
     </tests>
@@ -377,5 +377,5 @@
 @STACKS_INFOS@
 ]]>
     </help>
-    <expand macro="citation" />
+    <expand macro="citation"/>
 </tool>