--- a/stringtie.xml	Tue Nov 30 11:01:34 2021 +0000
+++ b/stringtie.xml	Wed Jul 27 09:28:15 2022 +0000
@@ -277,7 +277,7 @@
                 <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.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure fraction option works -->
         <test expect_num_outputs="1">
@@ -286,7 +286,7 @@
                 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
             </conditional>            
             <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure guide option works -->
         <test expect_num_outputs="1">
@@ -297,7 +297,7 @@
             <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.gtf" ftype="gtf" lines_diff="4"  />
+            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure guide with fraction works -->
         <test expect_num_outputs="1">
@@ -309,7 +309,7 @@
             <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.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure coverage and output for Ballgown works -->
         <test expect_num_outputs="7">
@@ -327,8 +327,8 @@
             <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="4" />
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
+            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure output for edgeR works -->
         <test expect_num_outputs="5">
@@ -346,8 +346,8 @@
             <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="4" />
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
+            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure gene abundances output works -->
         <test expect_num_outputs="2">
@@ -360,7 +360,7 @@
             <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.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
             <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
         </test>
         <!--Ensure another fraction value works -->
@@ -373,7 +373,7 @@
             <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="4" />
+            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure built-in GTFs work -->
         <test expect_num_outputs="1">
@@ -384,7 +384,7 @@
             <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="4" />
+            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test long reads input -->
         <test expect_num_outputs="1">
@@ -395,7 +395,7 @@
             <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="4" />
+            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test error splice option -->
         <test expect_num_outputs="1">
@@ -407,7 +407,7 @@
             <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="4" />
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf"  compare="re_match" sort="true"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
@@ -416,7 +416,7 @@
                 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
             </conditional>            
-            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
     </tests>
     <help><![CDATA[