--- a/mash_screen.xml	Tue Aug 31 09:21:03 2021 +0000
+++ b/mash_screen.xml	Thu Sep 11 10:21:48 2025 +0000
@@ -1,13 +1,11 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01">
-    <description>determines how well query sequences are contained within a pool of sequences</description>
-    <xrefs>
-        <xref type="bio.tools">mash</xref>
-    </xrefs>
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
+    <description>Determine sequence conservation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="xref"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
           ln -s '$queries_input_source.queries.fields.path' queries.msh &&
@@ -59,38 +57,49 @@
                 </param>
             </when>
             <when value="history">
-                <param name="queries" type="data" format="msh" />
+                <param name="queries" type="data" format="msh"/>
             </when>
         </conditional>
-        <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
-            help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
-        <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
-        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
+        <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
+        <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report"/>
+        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report"/>
     </inputs>
     <outputs>
-        <data name="output" format="tabular" />
+        <data name="output" format="tabular"/>
     </outputs>
     <tests>
-        <test>
-            <param name="queries_input_source_selector" value="history"/>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
-            <param name="pool_input_selector" value="single"/>
-            <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="single"/>
+                <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="history"/>
+                <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
         </test>
-        <test>
-            <param name="queries_input_source_selector" value="tool_data_table"/>
-            <param name="queries" value="test_sketch"/>
-            <param name="pool_input_selector" value="single"/>
-            <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="single"/>
+                <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="tool_data_table"/>
+                <param name="queries" value="test_sketch"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
         </test>
-        <test>
-            <param name="queries_input_source_selector" value="history"/>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
-            <param name="pool_input_selector" value="paired"/>
-            <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-            <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="paired"/>
+                <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+                <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="history"/>
+                <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
         </test>
     </tests>