From 73aa4909139901d2f3941749a34b1082fd4559d1 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Thu, 18 Jul 2024 11:12:56 +0200
Subject: [PATCH] Updated test cases

---
 tools/mitohifi/mitohifi.xml | 177 ++++++++++++++++++------------------
 1 file changed, 89 insertions(+), 88 deletions(-)

diff --git a/tools/mitohifi/mitohifi.xml b/tools/mitohifi/mitohifi.xml
index ba4795d220..aefb97304e 100644
--- a/tools/mitohifi/mitohifi.xml
+++ b/tools/mitohifi/mitohifi.xml
@@ -211,14 +211,14 @@
             </conditional>
             <output name="fasta_reference" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15593"/>
-                    <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/>
+                    <has_size value="15662"/>
+                    <has_line line=">PP230663.1 Spodoptera frugiperda isolate HC93 mitochondrion, complete genome"/>
                 </assert_contents>
             </output>
             <output name="genbank_reference" ftype="genbank">
                 <assert_contents>
-                    <has_size value="43220"/>
-                    <has_line line="DEFINITION  Condica capensis mitochondrion, complete genome."/>
+                    <has_size value="36693"/>
+                    <has_line line="DEFINITION  Spodoptera frugiperda isolate HC93 mitochondrion, complete genome."/>
                 </assert_contents>
             </output>
         </test>
@@ -265,7 +265,7 @@
                 </assert_contents>
             </output>
         </test>-->
-        <!--Test 03-->
+         <!--Test 02-->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -282,36 +282,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test>
-        <!--Test 04--> 
+        <!--Test 03--> 
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -328,36 +328,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="30768"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="53052"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 05 Testing -a functionality -->
+        <!--Test 04 (Testing -a flag)--> 
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -375,36 +375,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="30768"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="53052"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 06 -->
+        </test> 
+        <!--Test 05 -->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -421,36 +421,37 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 07 -->
+
+        <!--Test 06 -->
         <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -467,52 +468,52 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <!--<has_line line=">m64094_200908_163909/1605/ccs"/>-->
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="parsed_blast" ftype="txt">
                 <assert_contents>
-                    <has_size value="104"/>
+                    <has_size value="105"/>
                  </assert_contents>
             </output>
             <output name="parsed_blast_all" ftype="txt">
                 <assert_contents>
-                    <has_size value="104"/>
+                    <has_size value="105"/>
                 </assert_contents>
             </output>
             <output name="contigs_ids" ftype="txt">
                 <assert_contents>
                     <has_size value="11"/>
-                    <has_line line="ptg000001c"/>
+                    <has_line line="ptg000001l"/>
                 </assert_contents>
             </output>
         </test>
-        <!--Test 08 -->
+        <!--Test 07 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -529,41 +530,41 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="contigs_circularization" ftype="txt">
                 <assert_contents>
-                    <has_size value="28"/>
+                    <has_size value="55"/>
                 </assert_contents>
             </output>
-        </test> 
-        <!--Test 09 -->
+        </test>
+        <!--Test 08 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -580,42 +581,42 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="final_mitogenome" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="55"/>
+                    <!-- <has_line line=">ptg000001c"/> -->
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 10 -->
+        <!--Test 09 -->
         <test expect_num_outputs="2">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -639,8 +640,8 @@
                     <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
                 </assert_contents>
             </output>
-        </test> 
-        <!--Test 11 -->
+        </test>
+        <!--Test 10 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -655,40 +656,40 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="zip_file" ftype="zip">
                 <assert_contents>
-                    <has_size value="5418006" delta="100"/>
+                    <has_size value="5190456" delta="100"/>
                 </assert_contents>
             </output>
-        </test>
+        </test>     
     </tests>
     <help><![CDATA[
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