--- a/ivar_removereads.xml	Wed Jul 13 15:20:33 2022 +0000
+++ b/ivar_removereads.xml	Wed Jan 11 09:56:04 2023 +0000
@@ -1,12 +1,10 @@
-<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01">
+<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
     <description>Remove reads from trimmed BAM file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="3.8.1">python</requirement>
-    </expand>
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input_bed' binding_sites.bed &&
         python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
@@ -31,10 +29,10 @@
     <inputs>
         <param name="input_bam" argument="-i" type="data" format="bam"
         label="Bam input"
-        help="BAM dataset, preprocessed with ivar trim, to remove reads from" />
+        help="BAM dataset, preprocessed with ivar trim, to remove reads from"/>
         <param name="variants_tsv" type="data" format="tabular"
         label="Variants input"
-        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." />
+        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS."/>
         <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
         help="The same six-column BED dataset that served as input to ivar trim"/>
         <conditional name="amplicons">
@@ -59,19 +57,27 @@
             <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
             <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
             <conditional name="amplicons">
-                <param name="computed" value="no" />
+                <param name="computed" value="no"/>
                 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
             </conditional>
-            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+            <output name="output_bam" ftype="bam">
+                <assert_contents>
+                    <has_size value="3185672" delta="1000"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
             <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
             <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
             <conditional name="amplicons">
-                <param name="computed" value="yes" />
+                <param name="computed" value="yes"/>
             </conditional>
-            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+            <output name="output_bam" ftype="bam">
+                <assert_contents>
+                    <has_size value="3185672" delta="1000"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[