# HG changeset patch
# User iuc
# Date 1699649487 0
# Node ID a6f004bc73bfec9ecb19e2bb2100f572ad84e75c
# Parent  5ae13a1562715bc9a4966bbf871a8ffef07155f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84

diff -r 5ae13a156271 -r a6f004bc73bf generate_cannot_links.xml
--- a/generate_cannot_links.xml	Mon Mar 27 08:26:36 2023 +0000
+++ b/generate_cannot_links.xml	Fri Nov 10 20:51:27 2023 +0000
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 @FASTA_FILES@
-SemiBin
+SemiBin2
     generate_cannot_links
     --input-fasta 'contigs.fasta'
     --output 'output'
diff -r 5ae13a156271 -r a6f004bc73bf macros.xml
--- a/macros.xml	Mon Mar 27 08:26:36 2023 +0000
+++ b/macros.xml	Fri Nov 10 20:51:27 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" />