--- a/stacks_tsv2bam.xml	Tue Apr 27 09:28:24 2021 +0000
+++ b/stacks_tsv2bam.xml	Wed Sep 01 11:32:48 2021 +0000
@@ -3,7 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.13">samtools</requirement>
+    </expand>
     <expand macro="version_cmd"/>
     <command detect_errors="aggressive"><![CDATA[
 @FASTQ_INPUT_FUNCTIONS@
@@ -48,6 +50,9 @@
 2>&1
 
 && mv stacks_inputs/*matches.bam stacks_outputs
+
+## see comment in gstacks
+&& for b in stacks_outputs/*matches.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
 ]]></command>
 
     <inputs>
@@ -66,7 +71,7 @@
     </outputs>
 
     <tests>
-       <!-- test wo paired end data -->
+       <!-- test wo paired end data (this is not the default used in denovomap .. which is used for generating the test data therefore we only test if a list of two bams is generated) -->
        <test expect_num_outputs="2">
             <param name="input_cat">
                 <collection type="list">
@@ -93,10 +98,39 @@
             </param>
             <param name="add_log" value="yes"/>
             <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>
-            <output_collection name="bams" type="list" count="2">
-                <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
-                <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
-            </output_collection>
+            <output_collection name="bams" type="list" count="2"/>
+        </test>
+        <!-- test w popmap, w reverse reads as multiple selection -->
+       <test expect_num_outputs="2">
+            <param name="input_cat">
+                <collection type="list">
+                    <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
+                    <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
+                    <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
+               </collection>
+            </param>
+            <param name="input_stacks">
+                <collection type="list">
+                    <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
+                    <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
+                    <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
+                    <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
+                    <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
+                    <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
+               </collection>
+            </param>
+            <param name="input_matches">
+                <collection type="list">
+                    <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
+                    <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
+               </collection>
+            </param>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="input_type|input_type_select" value="single"/>
+            <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
+            <param name="add_log" value="yes"/>
+            <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
+            <output_collection name="bams" type="list" count="2"/>
         </test>
         <!-- test w popmap, w reverse reads as multiple selection -->
        <test expect_num_outputs="2">