--- a/hifiasm_meta.xml	Thu Jan 12 23:07:53 2023 +0000
+++ b/hifiasm_meta.xml	Wed Jan 18 09:12:38 2023 +0000
@@ -1,5 +1,5 @@
 <tool id="hifiasm_meta" name="Hifiasm_meta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
-    <description>for metagenome assembly using Hifi reads.</description>
+    <description>for metagenome assembly using Hifi reads</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -21,21 +21,24 @@
         --lowq-3 '$read_selection.lowq_3'
         --lowq-5 '$read_selection.lowq_5'
         -a '$assembly.a'
+        #if $f:
+            -f '$f'
+        #end if
         -k '$overlap_correction.k'
         -o asm
         -r '$overlap_correction.r'
-        #if '$read_selection.S':
-            -S
-        #end if
+        $read_selection.S
         -t \${GALAXY_SLOTS:-4}
         '$reads_fn'
 
     ]]></command>
     <inputs>
-        <!-- fastq files (could be a repeat or a collection) -->
         <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
+        <!-- This hidden parameter is only used to save RAM for planemo test. -->
+        <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
+        <param type="hidden" optional="true" argument="-f" />
         <section name="read_selection" title="Read selection" expanded="false">
-            <param argument='-S' type="boolean" checked="true" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." />
+            <param argument='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." />
             <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." />
             <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." />
             <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." />
@@ -51,8 +54,8 @@
     <outputs>
         <!-- contig graph files -->
         <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs">
+            <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" />
             <data name="Alternate contigs" label="Alternate contigs" from_work_dir="asm.a_ctg.gfa" format="gfa2" />
-            <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" />
         </collection>
         <!-- unitig graph files -->
         <collection name="unitig_graphs" type="list" label="hifiasm_meta on ${on_string}: unitig graphs">
@@ -68,8 +71,7 @@
         <!-- 01: basic function -->
         <test>
             <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
-            <param name='S' value="False" />
-            <param name='r' value="1" />
+            <param name='f' value="0" />
             <output_collection name="contig_graphs" type="list">
                 <element name="Primary contigs" file="asm.p_ctg.gfa"/>
                 <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
@@ -80,19 +82,21 @@
 hifiasm_meta
 ------------
 
-de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
+de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo
+assembler for PacBio Hifi reads.
 
 
-Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio
-Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
-genome. Thus, it is able to keep the haplotype information as much as possible.
-The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its
-outputs consist of multiple types of assembly graph in GFA format.
+Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio Hifi
+reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
+genome. Thus, it is able to keep the haplotype information as much as
+possible. The input of hifiasm is the PacBio Hifi reads in fasta/fastq
+format, and its outputs consist of multiple types of assembly graph in GFA
+format.
 
-Hifiasm_meta is a fork of hifiasm. It comes with a read selection module, which
-enables the assembly of dataset of high redundancy without compromising overall
-assembly quality, and meta-centric graphcleaning modules. Currently hifiasm_meta 
-does not take bining info.
+Hifiasm_meta is a fork of hifiasm. It comes with a read selection module,
+which enables the assembly of dataset of high redundancy without compromising
+overall assembly quality, and meta-centric graphcleaning modules. Currently
+hifiasm_meta does not take binning info.
 
 --------------
 
@@ -101,4 +105,5 @@
 
 This tool was wrapped by the Galaxy Australia team.
         ]]></help>
-</tool>
\ No newline at end of file
+        <expand macro="citations"/>
+</tool>