# HG changeset patch
# User iuc
# Date 1699649457 0
# Node ID ff4e487f4f7ea41d3a38df1b7e1dd9e9991c2308
# Parent  0ae1a2636de5304e1274825a5373d64e197e672a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84

diff -r 0ae1a2636de5 -r ff4e487f4f7e generate_sequence_features.xml
--- a/generate_sequence_features.xml	Mon Mar 27 08:24:19 2023 +0000
+++ b/generate_sequence_features.xml	Fri Nov 10 20:50:57 2023 +0000
@@ -13,7 +13,7 @@
 @BAM_FILES@
 @FASTA_FILES@
 
-SemiBin
+SemiBin2
 #if $mode.select == 'single' or $mode.select == 'co'
     generate_sequence_features_single
 #else
@@ -33,6 +33,7 @@
         <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 0ae1a2636de5 -r ff4e487f4f7e macros.xml
--- a/macros.xml	Mon Mar 27 08:24:19 2023 +0000
+++ b/macros.xml	Fri Nov 10 20:50:57 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.5.1</token>
+    <token name="@TOOL_VERSION@">2.0.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -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 $mode.multi_fasta.min_len
 &&
 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
@@ -222,7 +223,8 @@
     </xml>
     <xml name="orf-finder">
         <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
-            <option value="prodigal" selected="true">Prodigal</option>
+            <option value="fast-naive" selected="true">Fast-Naive</option>
+            <option value="prodigal">Prodigal</option>
             <option value="fraggenescan">Fraggenescan</option>
         </param>
     </xml>
@@ -251,8 +253,8 @@
     <xml name="minfasta-kbs">
         <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
     </xml>
-    <xml name="no-recluster">
-        <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/>
+    <xml name="write_pre_reclustering_bins">
+        <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
     </xml>
     <xml name="data">
         <param argument="--data" type="data" format="csv" label="Train data"/>
@@ -310,6 +312,7 @@
             <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
         </collection>
+        
     </xml>
     <xml name="train_output">
         <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />