# HG changeset patch
# User iuc
# Date 1742918021 0
# Node ID 68d2cd0be567ce4fb31d614274cb0b4121f6ad8f
# Parent  a6f004bc73bfec9ecb19e2bb2100f572ad84e75c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b

diff -r a6f004bc73bf -r 68d2cd0be567 generate_cannot_links.xml
--- a/generate_cannot_links.xml	Fri Nov 10 20:51:27 2023 +0000
+++ b/generate_cannot_links.xml	Tue Mar 25 15:53:41 2025 +0000
@@ -18,11 +18,12 @@
     --cannot-name 'cannot'
 #if $mode.ref.select == "cached"
     --reference-db-data-dir '$mode.ref.cached_db.fields.path'
-#else
+#end if
+#if $mode.ref.select == "taxonomy"
     --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
 #end if
     @MIN_LEN@
-#if str($ml_threshold) != ''
+#if $ml_threshold:
     --ml-threshold $ml_threshold
 #end if
     --cannot-name 'cannot'
@@ -34,15 +35,15 @@
             <expand macro="mode_select"/>
             <when value="single">
                 <expand macro="input-fasta-single"/>
-                <expand macro="ref-single"/>
+                <expand macro="ref-single-cannot"/>
             </when>
             <when value="co">
                 <expand macro="input-fasta-single"/>
-                <expand macro="ref-single"/>
+                <expand macro="ref-single-cannot"/>
             </when>
             <when value="multi">
                 <expand macro="input-fasta-multi"/>
-                <expand macro="ref-multi"/>
+                <expand macro="ref-multi-cannot"/>
             </when>
         </conditional>
         <expand macro="min_len"/>
@@ -65,7 +66,6 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
                     <has_text text="g1k_0,g4k_0"/>
@@ -87,7 +87,6 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
                     <has_text text="g1k_0,g4k_0"/>
@@ -101,7 +100,7 @@
                 <param name="select" value="single"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
                 <conditional name="ref">
-                    <param name="db_selector" value="cached"/>
+                    <param name="select" value="cached"/>
                     <param name="cached_db" value="test-db"/>
                 </conditional>
             </conditional>
@@ -109,11 +108,9 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
-                    <has_text text="g1k_0,g2k_0"/>
-                    <has_text text="g2k_9,g4k_1"/>
+                    <has_n_lines n='300' delta="10"/>
                 </assert_contents>
             </output>
         </test>
diff -r a6f004bc73bf -r 68d2cd0be567 macros.xml
--- a/macros.xml	Fri Nov 10 20:51:27 2023 +0000
+++ b/macros.xml	Tue Mar 25 15:53:41 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">