--- a/normalize-by-median.xml	Mon Jun 17 11:47:23 2024 +0000
+++ b/normalize-by-median.xml	Thu Oct 03 13:46:42 2024 +0000
@@ -1,10 +1,10 @@
 <tool id="khmer_normalize_by_median" name="khmer: Normalize By Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Filter reads using digital normalization via k-mer abundances</description>
-    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">normalize-by-median.py</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version" />
@@ -49,18 +49,18 @@
             label="Optional k-mer countgraph"
             help="The inputs file(s) will be processed using the kmer counts in the specified k-mer countgraph file as a starting point." />
         <param argument="--savegraph" name="save_countgraph" type="boolean" label="Save the k-mer countgraph(s) in a file" help="" />
-        <param argument="--cutoff" name="cutoff" type="integer" min="1" value="20" label="Cutoff" help="" />
+        <param argument="--cutoff" type="integer" min="1" value="20" label="Cutoff" help="" />
         <expand macro="tableinputs" />
     </inputs>
     <outputs>
-        <data name="countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
+        <data name="countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
             <filter>save_countgraph == True</filter>
         </data>
-        <data name="report" format="txt" label="${tool.name} report" />
+        <data name="report" format="csv" label="${tool.name} on ${on_string}: report" />
         <expand macro="output_sequences" extension="keep"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputs" value="test-abund-read-2.fa" ftype="fasta"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="1" />
@@ -74,7 +74,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputs" value="test-abund-read-2.fa.gz"  ftype="fasta.gz"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="2" />
@@ -89,12 +89,13 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="inputs" value="test-abund-read-paired.fa" ftype="fasta"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="1" />
             <param name="ksize" value="17" />
             <param name="paired" value="true" />
+            <param name="save_countgraph" value="true"/>
             <output name="report" file="normalize-by-median.paired.report.txt" />
             <output_collection name="sequences" type="list">
                 <element name="test-abund-read-paired.fa" ftype="fasta">
@@ -104,6 +105,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="countgraph">
+                <assert_contents>
+                    <has_size size="1k"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[