--- a/yahs.xml	Wed Jul 27 09:26:18 2022 +0000
+++ b/yahs.xml	Wed Sep 28 09:41:02 2022 +0000
@@ -1,8 +1,8 @@
 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>yet another HI-C scaffolding tool</description>
     <macros>
-        <token name="@VERSION@">1.2a</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION@">1.2a.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">yahs</requirement>
@@ -22,7 +22,7 @@
             #end if
             samtools faidx input.fasta &&
             mkdir initial_break agp_out agp_break final_outs &&
-            yahs input.fasta 
+            yahs --no-mem-check input.fasta 
             #if $function.bfile.ext == "bam":
                 input.bam
             #else if $function.bfile.ext == "bed":
@@ -152,6 +152,7 @@
         </data>
     </outputs>
     <tests>
+        <!-- TEST 1 -->
         <test expect_num_outputs="5">
             <conditional name="function">
                 <param name="function_select" value="yahs"/>
@@ -164,6 +165,7 @@
             <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
             <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
         </test>
+        <!-- TEST 2 -->
         <test expect_num_outputs="5">
             <conditional name="function">
                 <param name="function_select" value="yahs"/>
@@ -179,44 +181,44 @@
             </output_collection>
             <!-- COMMAND:  yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 -->
         </test>
+        <!-- TEST 3 -->
+        <test expect_num_outputs="6">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test2.fasta"/>
+                <param name="bfile" value="test2.bam"/>
+                <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
+                <conditional name="enzyme_conditional">
+                    <param name="enzyme_options" value="not_specified"/>
+                </conditional>
+            </conditional>
+            <param name="log_out" value="yes"/>
+	    <output name="log_file" ftype="txt">
+            <assert_contents>
+                <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6297 intra links + 102 inter links" />
+            </assert_contents>
+	    </output>
+            <!-- COMMAND:  yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 -->
+        </test>
+        <!-- TEST 4 -->
         <test expect_num_outputs="5">
             <conditional name="function">
                 <param name="function_select" value="yahs"/>
-                <param name="fasta" value="test.fasta"/>
-                <param name="bfile" value="test.bam"/>
+                <param name="fasta" value="test2.fasta"/>
+                <param name="bfile" value="test2.bed"/>
                 <param name="qual" value="10"/>
                 <param name="length" value="20"/>
                 <conditional name="enzyme_conditional">
-                    <param name="enzyme_options" value="specific"/>
-                    <param name="manual_enzyme" value="GATC,GANT"/>
+                    <param name="enzyme_options" value="not_specified"/>
                 </conditional>
             </conditional>
-            <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>
-            <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>
-            <output_collection name="initial_agp_break">
-                <element name="yahs_out_inital_break_01" file="test_03_initial_break.agp" ftype="agp"/>
-            </output_collection>
-            <!-- COMMAND:  yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 -->
-        </test>
-                <test expect_num_outputs="5">
-            <conditional name="function">
-                <param name="function_select" value="yahs"/>
-                <param name="fasta" value="test.fasta"/>
-                <param name="bfile" value="test.bam"/>
-                <param name="qual" value="10"/>
-                <param name="length" value="20"/>
-                <conditional name="enzyme_conditional">
-                    <param name="enzyme_options" value="preconfigured"/>
-                    <param name="preconfigured_enzymes" value="arima1"/>
-                </conditional>
-            </conditional>
-            <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>
-            <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>
+            <output name="final_agp_out" file="test_04_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_04_scaffolds_final.fa" ftype="fasta"/>
             <output_collection name="initial_agp_break">
                 <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>
             </output_collection>
-            <!-- COMMAND:  yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 -->
         </test>
+        <!-- TEST 5 -->
         <test expect_num_outputs="1">
             <conditional name="function">
                 <param name="function_select" value="agp_to_fasta"/>
@@ -227,6 +229,7 @@
             <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
             <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
         </test>
+        <!-- TEST 6 -->
         <test expect_num_outputs="6">
             <conditional name="function">
                 <param name="function_select" value="yahs"/>