fix hic mode (#1193)

* fix hic mode

* fix tests

* increase tool version

tools/hifiasm/hifiasm.xml

@@ -2,7 +2,7 @@
     <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
     <macros>
         <token name="@TOOL_VERSION@">0.16.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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" />
@@ -220,7 +220,8 @@
                 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
                 <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" />
                 <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" />
-                <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g">
+                <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
+                       help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g">
                     <sanitizer invalid_char="">
                         <valid initial="string.digits">
                             <add value="k" />
@@ -271,10 +272,10 @@
         <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
-        <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.bp.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
+        <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
-        <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
+        <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
         <!--Trio outputs with Hi-c reads-->
@@ -354,12 +355,14 @@
             <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
             <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
                 <assert_contents>
-                    <has_size value="0"/>
+                    <has_text_matching expression="^S" />
+                    <has_size value="59529" delta="500"/>
                 </assert_contents>
             </output>
             <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
                 <assert_contents>
-                    <has_size value="0"/>
+                    <has_text_matching expression="^S" />
+                    <has_size value="59529" delta="500"/>
                 </assert_contents>
             </output>
         </test>