--- a/extract-partitions.xml	Tue Aug 31 09:13:16 2021 +0000
+++ b/extract-partitions.xml	Thu Oct 03 13:45:20 2024 +0000
@@ -1,10 +1,10 @@
 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Separate sequences that are annotated with partitions into grouped files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">extract-partitions.py</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version" />
@@ -23,7 +23,7 @@
     </command>
     <inputs>
         <expand macro="input_sequences_filenames" />
-        <param argument="--max-size" name="max_size" type="integer" label="Max group size" value="1000000"
+        <param argument="--max-size" type="integer" label="Max group size" value="1000000"
             help="No more than this many number of sequences will be stored in each output"/>
         <param name="min_partition_size" type="integer" label="Min partition size" value="5"
             help="The minimum partition size worth keeping (--min-partition-size/-m)" />
@@ -31,15 +31,20 @@
             label="Output unassigned sequences" help="(--output-unassigned/-U)" />
     </inputs>
     <outputs>
-        <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
-        <collection name="groups-of-partitions" type="list">
-            <discover_datasets pattern="__name__" directory="output" />
+        <data name="distribution" format="txt" from_work_dir="output/output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
+        <collection name="groups_of_partitions" type="list" format="fasta">
+            <discover_datasets pattern="__name__" directory="output" format="fasta"/>
         </collection>
     </outputs>
     <tests>
         <test>
             <param name="inputs" value="random-20-a.fa.part"/>
-            <output_collection name="groups-of-partitions">
+            <output name="distribution">
+                <assert_contents>
+                    <has_text text="99 1 1 99"/>
+                </assert_contents>
+            </output>
+            <output_collection name="groups_of_partitions">
                 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
             </output_collection>
         </test>