diff --git a/tools/stringtie/stringtie.xml b/tools/stringtie/stringtie.xml
index ee03c9630e0..8976cbe7f69 100644
--- a/tools/stringtie/stringtie.xml
+++ b/tools/stringtie/stringtie.xml
@@ -278,7 +278,7 @@ $adv.multi_mapping
                 <param name="input_mode" value="short_reads"/>
                 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>
-            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure fraction option works -->
         <test expect_num_outputs="1">
@@ -287,7 +287,7 @@ $adv.multi_mapping
                 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
             <param name="fraction" value="0.17"/>
-            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure guide option works -->
         <test expect_num_outputs="1">
@@ -298,7 +298,7 @@ $adv.multi_mapping
             <param name="use_guide" value="yes"/>
             <param name="guide_gff_select" value="history"/>
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure guide with fraction works -->
         <test expect_num_outputs="1">
@@ -310,7 +310,7 @@ $adv.multi_mapping
             <param name="guide_gff_select" value="history"/>
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
             <param name="fraction" value="0.17"/>
-            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure coverage and output for Ballgown works -->
         <test expect_num_outputs="7">
@@ -328,8 +328,8 @@ $adv.multi_mapping
             <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular"/>
             <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular"/>
             <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular"/>
-            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2"/>
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure output for edgeR works -->
         <test expect_num_outputs="5">
@@ -347,8 +347,8 @@ $adv.multi_mapping
             <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular"/>
             <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular"/>
             <output name="legend" file="legend.tsv" ftype="tabular"/>
-            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2"/>
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure gene abundances output works -->
         <test expect_num_outputs="2">
@@ -361,8 +361,8 @@ $adv.multi_mapping
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
             <param name="fraction" value="0.17"/>
             <param name="abundance_estimation" value="true"/>
-            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/>
-            <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="4"/>
+            <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="4" />
         </test>
         <!--Ensure another fraction value works -->
         <test expect_num_outputs="1">
@@ -374,7 +374,7 @@ $adv.multi_mapping
             <param name="guide_gff_select" value="history"/>
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
             <param name="fraction" value="0.15"/>
-            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!--Ensure built-in GTFs work -->
         <test expect_num_outputs="1">
@@ -385,7 +385,7 @@ $adv.multi_mapping
             <param name="use_guide" value="yes"/>
             <param name="guide_gff_select" value="cached"/>
             <param name="fraction" value="0.15"/>
-            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!-- Test long reads input -->
         <test expect_num_outputs="1">
@@ -396,7 +396,7 @@ $adv.multi_mapping
             <param name="use_guide" value="yes"/>
             <param name="guide_gff_select" value="cached"/>
             <param name="fraction" value="0.15"/>
-            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!-- Test error splice option -->
         <test expect_num_outputs="1">
@@ -408,7 +408,7 @@ $adv.multi_mapping
             <param name="use_guide" value="yes"/>
             <param name="guide_gff_select" value="cached"/>
             <param name="fraction" value="0.15"/>
-            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
diff --git a/tools/stringtie/stringtie_merge.xml b/tools/stringtie/stringtie_merge.xml
index 96e5a051c14..13749beaa34 100644
--- a/tools/stringtie/stringtie_merge.xml
+++ b/tools/stringtie/stringtie_merge.xml
@@ -43,7 +43,7 @@
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/>
             <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/>
-            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>