# HG changeset patch
# User iuc
# Date 1741695785 0
# Node ID 6f7211f93b0616ae471faed2929ea8d1592da94f
# Parent  2a8bc1d26d06020cd6669eb9d037e04190589e02
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 0f381ce2cdb0683f1bc8e1da321a5a75440bf619

diff -r 2a8bc1d26d06 -r 6f7211f93b06 macros.xml
--- a/macros.xml	Thu Apr 11 21:56:14 2024 +0000
+++ b/macros.xml	Tue Mar 11 12:23:05 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
diff -r 2a8bc1d26d06 -r 6f7211f93b06 metawrapmg_binning.xml
--- a/metawrapmg_binning.xml	Thu Apr 11 21:56:14 2024 +0000
+++ b/metawrapmg_binning.xml	Tue Mar 11 12:23:05 2025 +0000
@@ -16,13 +16,10 @@
         ##################
 
         ## only plain FASTA and FASTQ
-        ln -s '$metagenome' metagenome.fasta
-        &&
+        ln -s '$metagenome' metagenome.fasta &&
         ## Metawrap checks for files named _1.fastq and _2.fastq.
-        ln -s '$input_1' reads_1.fastq
-        &&
-        ln -s '$input_2' reads_2.fastq
-        &&
+        ln -s '$input.forward' reads_1.fastq &&
+        ln -s '$input.reverse' reads_2.fastq &&
 
         #####################
         ## INITIAL BINNING ##
@@ -71,8 +68,7 @@
     ]]></command>
     <inputs>
         <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/>
-        <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1."/>
-        <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2."/>
+        <param name="input" type="data_collection" collection_type="paired" label="Reads" help="Original reads that were used for the assembly"/>
         <section name="binning" title="Binning parameters" expanded="false">
             <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>
             <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>
@@ -103,10 +99,16 @@
         <!-- 01: basic function -->
         <test>
             <param name="metagenome" value="subset.fasta.gz"/>
-            <param name="input_1" value="mapped_reads.r1.fastq.gz"/>
-            <param name="input_2" value="mapped_reads.r2.fastq.gz"/>
-            <param name="c" value="60"/>
-            <param name="x" value="15"/>
+            <param name="input">
+                <collection type="paired">
+                    <element name="forward" value="mapped_reads.r1.fastq.gz"/>
+                    <element name="reverse" value="mapped_reads.r2.fastq.gz"/>
+                </collection>
+            </param>
+            <section name="binning">
+                <param name="c" value="60"/>
+                <param name="x" value="15"/>
+            </section>
             <param name="hidden_quick" value="--quick"/>
             <output_collection name="metawrap_bins" type="list">
                 <element name="bin.1" ftype="fasta">