# HG changeset patch
# User iuc
# Date 1715609275 0
# Node ID cbf488da3b2c91816460f92654152619b3b05230
# Parent  8eb8750070d48933470277b10a3e47cfdf2aabf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 8dc7b89b32a9e86c48e9ef7078703ae277bdaf96

diff -r 8eb8750070d4 -r cbf488da3b2c macros.xml
--- a/macros.xml	Tue Apr 30 11:53:08 2024 +0000
+++ b/macros.xml	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.2</token>
+    <token name="@TOOL_VERSION@">2.2.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
diff -r 8eb8750070d4 -r cbf488da3b2c stringtie.xml
--- a/stringtie.xml	Tue Apr 30 11:53:08 2024 +0000
+++ b/stringtie.xml	Mon May 13 14:07:55 2024 +0000
@@ -278,7 +278,7 @@
                 <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_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 @@
                 <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 @@
             <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 -r 8eb8750070d4 -r cbf488da3b2c stringtie_merge.xml
--- a/stringtie_merge.xml	Tue Apr 30 11:53:08 2024 +0000
+++ b/stringtie_merge.xml	Mon May 13 14:07:55 2024 +0000
@@ -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"/>
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_merge_out1.gtf
--- a/test-data/stringtie_merge_out1.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_merge_out1.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/d/8/3/dataset_d8325888-f757-4336-9e42-1101c6ec296d.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/6/outputs/dataset_51c0f399-1d26-44c7-a4fd-e6f8897fe843.dat /tmp/tmpr8yl388j/files/5/5/b/dataset_55be25a6-c7f0-474e-a011-bb4cd427cfa2.dat /tmp/tmpr8yl388j/files/b/2/e/dataset_b2ef2a9d-3640-4858-8424-b4a29c57164d.dat /tmp/tmpr8yl388j/files/d/9/b/dataset_d9be016a-da47-4ad1-89bd-e9781f2751db.dat /tmp/tmpr8yl388j/files/b/e/f/dataset_befee6d4-95fb-4ee9-83a4-9b1302e6a21a.dat
-# StringTie version 2.2.2
+# stringtie --merge -p 1 -G /tmp/tmpapg328z2/files/2/f/f/dataset_2ff25b99-2996-4dec-83a0-d6c51a43761b.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpapg328z2/job_working_directory/000/6/outputs/dataset_edbe5c52-579b-47c1-b320-ba0bc8412b28.dat /tmp/tmpapg328z2/files/8/8/b/dataset_88be1713-81b3-46bd-ba7f-fa6cc8afca2d.dat /tmp/tmpapg328z2/files/b/c/d/dataset_bcd50081-e47a-48e9-ad3b-772cb04956b4.dat /tmp/tmpapg328z2/files/4/f/b/dataset_4fbad666-bf26-4724-92da-1b19fe88ba76.dat /tmp/tmpapg328z2/files/1/e/a/dataset_1ea206fb-8397-4b1d-9930-3341d6597970.dat
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; 
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; 
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; 
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_merge_out2.gtf
--- a/test-data/stringtie_merge_out2.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_merge_out2.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/9/2/b/dataset_92bbbdee-6cfa-4cff-bab3-0d0836475341.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/10/outputs/dataset_81bd1351-3b74-4332-b789-a4f53357a8fa.dat /tmp/tmpr8yl388j/files/3/c/3/dataset_3c3b1fdc-0351-48ef-a6eb-6c226751f619.dat /tmp/tmpr8yl388j/files/2/a/4/dataset_2a44d87f-131b-4587-bf25-2527d7d89964.dat
-# StringTie version 2.2.2
+# stringtie --merge -p 1 -G /tmp/tmpapg328z2/files/e/5/c/dataset_e5cafc26-99e9-441e-b6d7-6732d4e8ff0c.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpapg328z2/job_working_directory/000/10/outputs/dataset_c4d4110e-aa10-4a05-9ce8-bd76d91507a8.dat /tmp/tmpapg328z2/files/1/0/b/dataset_10b29ded-6b7b-45d4-8138-0ee6ebcbe3be.dat /tmp/tmpapg328z2/files/0/e/f/dataset_0efcd212-8978-444b-b29a-8818bb24f977.dat
+# StringTie version 2.2.3
 chr1	StringTie	transcript	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
 chr1	StringTie	exon	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 
 chr1	StringTie	transcript	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out10.gtf
--- a/test-data/stringtie_out10.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out10.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/8/4/7/dataset_84719807-dfbb-42a2-b1db-377469c94d05.dat -L -E 25 -o /tmp/tmpm2qmdax_/job_working_directory/000/26/outputs/dataset_4dfedf5d-98a8-4b6a-8f7d-1b6c2116bbd4.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/b/d/d/dataset_bdd549e2-f61f-41c5-8f58-c2c5a9fd4532.dat -L -E 25 -o /tmp/tmp0_r_zs0r/job_working_directory/000/26/outputs/dataset_deef7f55-a366-4d3e-b564-a787edc0e424.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.795303"; FPKM "3354967.250000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.777779";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "54.160000";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out11.gtf
--- a/test-data/stringtie_out11.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out11.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/c/e/f/dataset_cefc5152-4ac0-4e7e-9223-1b55c7b7ac85.dat -L -E 30 -o /tmp/tmpm2qmdax_/job_working_directory/000/28/outputs/dataset_5597b8ed-94cb-4345-9b86-8ad715fbe328.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/4/d/0/dataset_4d035599-e7f2-46dd-81bc-b3b05b7deddb.dat -L -E 30 -o /tmp/tmp0_r_zs0r/job_working_directory/000/28/outputs/dataset_0f86a5b1-39e9-428b-9707-403ec325a6d1.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 chr19	StringTie	transcript	567221	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812";
 chr19	StringTie	exon	567221	567648	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";
 chr19	StringTie	exon	571440	571596	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out1_re.gtf
--- a/test-data/stringtie_out1_re.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out1_re.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/7/c/4/dataset_7c4559ac-1803-4156-86aa-a965c40579dd.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/2/outputs/dataset_628e00eb-c42b-4122-af6b-138d203e2288.dat -p 1 -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/8/8/e/dataset_88e83131-016d-4ce3-b893-0f7de8d3af60.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/2/outputs/dataset_4eaceb01-9219-463e-bd84-48bb0abba00a.dat -p 1 -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out2_re.gtf
--- a/test-data/stringtie_out2_re.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out2_re.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/8/7/1/dataset_871b229a-6bb9-4fea-ad17-d71634870366.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/4/outputs/dataset_3a880427-cc94-440b-974f-61adfa148f55.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/a/4/e/dataset_a4ee773e-4f64-4581-9722-c49a00668024.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/4/outputs/dataset_c0a74da9-51d7-4ebe-b9bb-987e8e81c263.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out3_re.gtf
--- a/test-data/stringtie_out3_re.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out3_re.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/1/9/d/dataset_19d005b0-21af-4097-ba09-dcfd47a9639d.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/7/outputs/dataset_e7ff968a-b61b-4cce-900e-04fd85518371.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/9/f/f/dataset_9ffccc2e-ed5f-4cae-ada7-8dc31afedc6b.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/7/outputs/dataset_e3ac25d9-695a-438b-b79f-09ba03a56866.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out4_re.gtf
--- a/test-data/stringtie_out4_re.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out4_re.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/4/2/5/dataset_42595174-c98e-47c3-80d3-4e7f41bf639a.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_89f0738d-5fec-45ea-b655-2585a71d3d18.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 -A /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_793b9d71-4869-4258-a6a5-1d50bd53361f.dat
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/1/4/d/dataset_14d5e119-b917-4862-b08b-d22a834135fb.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/19/outputs/dataset_1432f44a-4723-48c7-88cd-717a7e8f5918.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 -A /tmp/tmp0_r_zs0r/job_working_directory/000/19/outputs/dataset_7975d0ad-9f63-49cc-9a87-47b0265aa260.dat
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out5.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/5/b/5/dataset_5b55cbd8-f515-46d6-b1d2-71201435248b.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_3b84d9d9-efe9-4d58-9f34-c6d3f5da763f.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_8fb2eb9a-4a6c-4300-9639-0a39336f7dab.dat -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/d/0/d/dataset_d0dfd219-9dc5-47c7-bb3e-d0a0751c4f8f.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/13/outputs/dataset_9a98f26d-1db3-49d9-80e7-755a92d2f17d.dat -p 1 -G guide.gff -C /tmp/tmp0_r_zs0r/job_working_directory/000/13/outputs/dataset_816761de-9208-416a-b240-adb727109d43.dat -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out6.gtf
--- a/test-data/stringtie_out6.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out6.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/5/f/e/dataset_5fe68ff0-f093-4d09-86ec-2e1a279bb301.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_821eef87-9397-4b49-8860-910104445af9.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_5a1ac870-b1e8-4437-8b57-211b71557c52.dat -e -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/6/f/0/dataset_6f0a4741-c3ba-4fea-8358-8d0cb87734d2.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/16/outputs/dataset_b53ba999-250c-412b-8076-fd66d941f98f.dat -p 1 -G guide.gff -C /tmp/tmp0_r_zs0r/job_working_directory/000/16/outputs/dataset_300c6a87-4de4-46cc-87c0-47ac26c85e86.dat -e -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out8.gtf
--- a/test-data/stringtie_out8.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out8.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/1/d/b/dataset_1db0e632-3580-4045-9441-56a6e90bafea.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/22/outputs/dataset_2072a123-60b0-41ed-b4fc-9df0db87bff0.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/3/2/a/dataset_32a35589-9235-45b0-ae61-1265dd110aa2.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/22/outputs/dataset_cd317961-2b7b-43a7-9459-f11d82ad2bad.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
diff -r 8eb8750070d4 -r cbf488da3b2c test-data/stringtie_out9.gtf
--- a/test-data/stringtie_out9.gtf	Tue Apr 30 11:53:08 2024 +0000
+++ b/test-data/stringtie_out9.gtf	Mon May 13 14:07:55 2024 +0000
@@ -1,5 +1,5 @@
-# stringtie /tmp/tmpm2qmdax_/files/c/8/7/dataset_c8776afe-26a8-48d2-bea6-b66d6a50a5ad.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/24/outputs/dataset_721fe1c9-4aea-4e2f-84d4-76e855eb610c.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
-# StringTie version 2.2.2
+# stringtie /tmp/tmp0_r_zs0r/files/c/5/0/dataset_c509b2c2-87bc-4bf0-b7ac-7235ed084a5a.dat -o /tmp/tmp0_r_zs0r/job_working_directory/000/24/outputs/dataset_10fbf44c-f1c4-45bd-960a-cd80ebc918f4.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";