--- a/hifiasm.xml	Tue Jan 24 17:46:39 2023 +0000
+++ b/hifiasm.xml	Thu Feb 23 22:34:21 2023 +0000
@@ -1,8 +1,8 @@
 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.18.5</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">0.18.8</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
         <xml name="reads">
             <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
@@ -117,8 +117,8 @@
         #end if
 
         #if str($hic_partition.hic_partition_selector) == 'set':
-            --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) }
-            --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) }
+            --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) }
+            --h2 ${ ','.join(["'%s'" % $x for $x in $hic2_inputs]) }
             #if $hic_partition.seed:
                 --seed $hic_partition.seed
             #end if
@@ -135,7 +135,7 @@
         #end if
 
         #if str($ont_integration.ont_integration_selector) == 'set':
-            --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) }
+            --ul ${ ','.join(["'%s'" % $x for $x in $ultralong_inputs]) }
             #if $ont_integration.ul_rate:
                 --ul-rate $ont_integration.ul_rate
             #end if
@@ -272,16 +272,16 @@
     </inputs>
     <outputs>
         <!--Standard mode-->
-        <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
+        <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
-        <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph">
+        <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
-        <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph">
+        <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
-        <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph">
+        <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
         <!--Trio outputs without Hi-c reads-->
@@ -291,10 +291,10 @@
         <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
-        <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
+        <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for HiC-phased assembly">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
-        <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph">
+        <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
         </data>
         <!-- Stardand mode with Hi-C partition outputs -->
@@ -314,10 +314,10 @@
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
         <!--Trio outputs with Hi-c reads-->
-        <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
+        <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
-        <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">
+        <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed unitig graph">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
         <!--Log output-->
@@ -499,11 +499,28 @@
 	        <param name="filter_bits" value="0" />
             <conditional name="ont_integration">
                 <param name="ont_integration_selector" value="set" />
-                <param name="ul" value="nanopore.first5.fasta.gz" />
+                <param name="ul" value="nanopore.fasta.gz" />
                 <param name="ul_tip" value="1" />
             </conditional>
-            <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" />
-            <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" />
+            <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1" />
+            <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1" />
+        </test>
+        <!-- TEST 13: test multi-file nanopore input -->
+        <test expect_num_outputs="6">
+            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
+            <param name="mode_selector" value="standard" />
+	        <param name="filter_bits" value="0" />
+            <param name="log_out" value="yes" />
+            <conditional name="ont_integration">
+                <param name="ont_integration_selector" value="set" />
+                <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz" />
+                <param name="ul_tip" value="1" />
+            </conditional>
+            <output name="log_file" ftype="txt">
+                <assert_contents>
+                    <has_text text="--ul ./ultralong/input_0.fasta.gz,./ultralong/input_1.fasta.gz"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[