--- a/hifiasm.xml	Tue Oct 25 18:13:16 2022 +0000
+++ b/hifiasm.xml	Fri Jan 20 22:27:43 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@">0.16.1</token>
-        <token name="@VERSION_SUFFIX@">4</token>
+        <token name="@TOOL_VERSION@">0.18.5</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" />
@@ -293,7 +293,7 @@
         <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
             <filter>log_out</filter>
         </data>
-        <collection name="noseq files" type="list" label="${tool.name} on ${on_string}: noseq files">
+        <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
             <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
         </collection>
     </outputs>
@@ -305,11 +305,6 @@
             <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <test expect_num_outputs="5">
             <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
@@ -318,11 +313,6 @@
             <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test logfile out-->
         <test expect_num_outputs="6">
@@ -333,14 +323,9 @@
             <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
             <output name="log_file" ftype="txt">
                 <assert_contents>
-                    <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
+                    <has_text text="-o output -f 0 --primary input_0.fasta.gz"/>
                 </assert_contents>
             </output>
         </test>
@@ -363,19 +348,19 @@
             <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
                 <assert_contents>
                     <has_text_matching expression="^S" />
-                    <has_size value="59529" delta="500"/>
+                    <has_size value="83914" delta="500"/>
                 </assert_contents>
             </output>
             <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
                 <assert_contents>
                     <has_text_matching expression="^S" />
-                    <has_size value="59529" delta="500"/>
+                    <has_size value="83914" delta="500"/>
                 </assert_contents>
             </output>
             <output name="hic_raw_initig" ftype="gfa1" >
                 <assert_contents>
                     <has_text_matching expression="^S" />
-                    <has_size value="59522" delta="500"/>
+                    <has_size value="83904" delta="500"/>
                 </assert_contents>
             </output>
         </test>
@@ -390,26 +375,11 @@
                 <param name="max_kmers" value="2"/>
                 <param name="min_kmers" value="5"/>
             </conditional>
-            <output name="raw_unitigs_trio" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
-            <output name="processed_unitigs_trio" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
-            <output name="hap1_contigs">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
-            <output name="hap2_contigs">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
+            <assert_command>
+                <has_text text="-1 hap1.yak" />
+                <has_text text="-2 hap2.yak" />
+                <has_text text="--primary" />
+            </assert_command>
         </test>
         <!-- Test ignore-error-corrected option -->
         <test expect_num_outputs="5">
@@ -423,11 +393,6 @@
             <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test expected haplotype number -->
         <test expect_num_outputs="5">
@@ -441,11 +406,6 @@
             <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test min_hist_cnt option -->
         <test expect_num_outputs="5">
@@ -459,11 +419,6 @@
             <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph"  ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test max_kooc option -->
         <test expect_num_outputs="5">
@@ -477,11 +432,6 @@
             <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph"  ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test hg-size option -->
         <test expect_num_outputs="5">
@@ -495,11 +445,6 @@
             <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph"  ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test ignore-error-corrected option -->
         <test expect_num_outputs="5">
@@ -513,11 +458,6 @@
             <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
             <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
             <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
-            <output name="alternate_contig_graph" ftype="gfa1">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
         </test>
     </tests>
     <help><![CDATA[