# HG changeset patch
# User iuc
# Date 1742917799 0
# Node ID f5aff7c9a65d6893708eaf94d360f0ec3422b858
# Parent  cae8e4d4f726be753c4f4022f178e407c0196aaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b

diff -r cae8e4d4f726 -r f5aff7c9a65d generate_sequence_features.xml
--- a/generate_sequence_features.xml	Mon Mar 27 08:21:02 2023 +0000
+++ b/generate_sequence_features.xml	Tue Mar 25 15:49:59 2025 +0000
@@ -13,7 +13,7 @@
 @BAM_FILES@
 @FASTA_FILES@
 
-SemiBin
+SemiBin2
 #if $mode.select == 'single' or $mode.select == 'co'
     generate_sequence_features_single
 #else
@@ -25,7 +25,7 @@
     --output 'output'
     --threads \${GALAXY_SLOTS:-1}
     @MIN_LEN@
-#if str($ml_threshold) != ''
+#if $ml_threshold:
     --ml-threshold $ml_threshold
 #end if
     ]]></command>
diff -r cae8e4d4f726 -r f5aff7c9a65d macros.xml
--- a/macros.xml	Mon Mar 27 08:21:02 2023 +0000
+++ b/macros.xml	Tue Mar 25 15:49:59 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.5.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>
@@ -15,7 +15,7 @@
         </requirements>
     </xml>
     <xml name="version">
-        <version_command>SemiBin -v</version_command>
+        <version_command>SemiBin2 -v</version_command>
     </xml>
     <xml name="mode_fasta_bam">
         <conditional name="mode">
@@ -109,10 +109,11 @@
             #end if
         #end for
 #set $separator = ':'
-SemiBin concatenate_fasta
+SemiBin2 concatenate_fasta
     --input-fasta *.fasta
     --output 'output'
     --separator '$separator'
+    --compression none
     -m $mode.multi_fasta.min_len
 &&
 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
@@ -139,9 +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>
@@ -152,6 +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"/>
@@ -161,6 +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">
@@ -172,6 +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">
@@ -183,6 +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">
@@ -222,7 +255,8 @@
     </xml>
     <xml name="orf-finder">
         <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
-            <option value="prodigal" selected="true">Prodigal</option>
+            <option value="fast-naive" selected="true">Fast-Naive</option>
+            <option value="prodigal">Prodigal</option>
             <option value="fraggenescan">Fraggenescan</option>
         </param>
     </xml>
@@ -251,8 +285,8 @@
     <xml name="minfasta-kbs">
         <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
     </xml>
-    <xml name="no-recluster">
-        <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/>
+    <xml name="write_pre_reclustering_bins">
+        <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
     </xml>
     <xml name="data">
         <param argument="--data" type="data" format="csv" label="Train data"/>
@@ -310,6 +344,7 @@
             <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
         </collection>
+        
     </xml>
     <xml name="train_output">
         <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />