--- a/ngsfilter.xml	Wed Sep 01 07:52:00 2021 +0000
+++ b/ngsfilter.xml	Thu Oct 30 16:02:48 2025 +0000
@@ -1,9 +1,9 @@
 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -34,10 +34,10 @@
         @GENERATE_GALAXY_JSON@
     ]]></command>
     <inputs>
-        <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample" />
-        <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend" />
-        <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)" />
-        <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?" />
+        <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample"/>
+        <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend"/>
+        <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)"/>
+        <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?"/>
         <expand macro="input_format_options_macro"/>
         <expand macro="out_format_macro"/>
     </inputs>
@@ -45,21 +45,21 @@
         <data name="unident"  format="auto" label="${tool.name} on ${on_string}: Unassigned sequences">
             <filter>bool is True</filter>
         </data>
-        <data name="output"  format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated" />
+        <data name="output"  format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated"/>
     </outputs>
     <tests>
-       <test>
+       <test expect_num_outputs="1">
            <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
-           <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger" />
+           <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger"/>
            <param name="mismatch" value="2" />
            <param name="bool" value="False" />
            <output name="output" file="output_ngsfilter.fastq" ftype="fastqsanger"/>
        </test>
-       <test>
-           <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
-           <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" />
-           <param name="mismatch" value="3" />
-           <param name="bool" value="True" />
+       <test expect_num_outputs="2">
+           <param name="inputextrafile" value="input_ngsfilter_extrafile.txt"/>
+           <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz"/>
+           <param name="mismatch" value="3"/>
+           <param name="bool" value="True"/>
            <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastqsanger.gz" decompress="true"/>
            <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastqsanger.gz" decompress="true"/>
        </test>