# HG changeset patch
# User iuc
# Date 1742917991 0
# Node ID 0608cf7dc52838c50d4c01b44cae62edc487c6c0
# Parent  ff4e487f4f7ea41d3a38df1b7e1dd9e9991c2308
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b

diff -r ff4e487f4f7e -r 0608cf7dc528 generate_sequence_features.xml
--- a/generate_sequence_features.xml	Fri Nov 10 20:50:57 2023 +0000
+++ b/generate_sequence_features.xml	Tue Mar 25 15:53:11 2025 +0000
@@ -25,7 +25,7 @@
     --output 'output'
     --threads \${GALAXY_SLOTS:-1}
     @MIN_LEN@
-#if str($ml_threshold) != ''
+#if $ml_threshold:
     --ml-threshold $ml_threshold
 #end if
     ]]></command>
@@ -33,7 +33,6 @@
         <expand macro="mode_fasta_bam"/>
         <expand macro="min_len"/>
         <expand macro="ml-threshold"/>
-
         <param name="extra_output" type="select" multiple="true" label="Extra outputs" help="In addition to the training data">
             <option value="coverage">Coverage files</option>
             <option value="contigs">Contigs (if multiple sample)</option>
diff -r ff4e487f4f7e -r 0608cf7dc528 macros.xml
--- a/macros.xml	Fri Nov 10 20:50:57 2023 +0000
+++ b/macros.xml	Tue Mar 25 15:53:11 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.0.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>
@@ -140,9 +140,16 @@
     #end for
 #end if
     ]]></token>
+    <xml name="ref_select_cannot">
+        <param name="select" type="select" label="Reference database">
+            <option value="cached">Cached database</option>
+            <option value="taxonomy">Pre-computed taxonomy</option>
+        </param>
+    </xml>
     <xml name="ref_select">
         <param name="select" type="select" label="Reference database">
-            <option value="cached" selected="true">Cached database</option>
+            <option value="ml" selected="true">Use SemiBin ML function</option>
+            <option value="cached">Cached database</option>
             <option value="taxonomy">Pre-computed taxonomy</option>
         </param>
     </xml>
@@ -153,6 +160,28 @@
             </options>
         </param>
     </xml>
+    <xml name="ref-single-cannot">
+        <conditional name="ref">
+            <expand macro="ref_select_cannot"/>
+            <when value="cached">
+                <expand macro="cached_db"/>
+            </when>
+            <when value="taxonomy">
+                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="ref-multi-cannot">
+        <conditional name="ref">
+            <expand macro="ref_select_cannot"/>
+            <when value="cached">
+                <expand macro="cached_db"/>
+            </when>
+            <when value="taxonomy">
+                <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="ref-single">
         <conditional name="ref">
             <expand macro="ref_select"/>
@@ -162,6 +191,7 @@
             <when value="taxonomy">
                 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
             </when>
+            <when value="ml"/>
         </conditional>
     </xml>
     <xml name="ref-multi">
@@ -173,6 +203,7 @@
             <when value="taxonomy">
                 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
             </when>
+            <when value="ml"/>
         </conditional>
     </xml>
     <xml name="ref_single">
@@ -184,6 +215,7 @@
             <when value="taxonomy">
                 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
             </when>
+            <when value="ml"/>
         </conditional>
     </xml>
     <xml name="min_len">