# HG changeset patch
# User iuc
# Date 1667246882 0
# Node ID 914cfcba0ec8283b5f33112dc261f4fc5772721f
# Parent  cef79931dda5de51b28103e22cc6e220ea6d69cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 8923485156dc1150213ad1f324aa16aaef4ae643

diff -r cef79931dda5 -r 914cfcba0ec8 macros.xml
--- a/macros.xml	Wed Jul 27 09:28:15 2022 +0000
+++ b/macros.xml	Mon Oct 31 20:08:02 2022 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.1.7</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
-        <requirement type="package" version="1.14">samtools</requirement>
+        <requirement type="package" version="1.16.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r cef79931dda5 -r 914cfcba0ec8 stringtie.xml
--- a/stringtie.xml	Wed Jul 27 09:28:15 2022 +0000
+++ b/stringtie.xml	Mon Oct 31 20:08:02 2022 +0000
@@ -11,6 +11,7 @@
     <expand macro="version_command" />
     <command><![CDATA[
 #import re
+#set $compressed = ("bam","cram")
 mkdir -p ./special_de_output/sample1/ &&
 
 ## Get Guide GTF/GFF if selected
@@ -34,12 +35,12 @@
         -E $input_options.error_splice
     #end if
 #else
-    #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam':
-        strigtie '$input_options.input_bam_short' '$input_options.input_bam_long'
-    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam':
+    #if $input_options.input_bam_short.file_ext in $compressed and $input_options.input_bam_long.file_ext in $compressed:
+        stringtie '$input_options.input_bam_short' '$input_options.input_bam_long'
+    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype in $compressed:
         samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
         && stringtie short_sorted.sam '$input_options.input_bam_long'
-    #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam':
+    #else if $input_options.input_bam_short.metadata.ftype in $compressed and $input_options.input_bam_long.metadata.ftype == 'sam':
         samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
         && stringtie'$input_options.input_bam_short' long_sorted.sam
     #else
@@ -143,15 +144,15 @@
                 <option value="mixed_reads">Mixed mode: short and long reads</option>
             </param>
             <when value="short_reads">
-                <param name="input_bam" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
+                <param name="input_bam" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
             </when>
             <when value="long_reads">
-                <param name="input_bam" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
+                <param name="input_bam" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
             </when>
             <when value="mixed_reads">
-                <param name="input_bam_short" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
-                <param name="input_bam_long" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
+                <param name="input_bam_short" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
+                <param name="input_bam_long" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
             </when>
         </conditional>
@@ -418,6 +419,20 @@
             </conditional>            
             <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
+        <!-- Test cram input -->
+        <test expect_num_outputs="1">
+            <conditional name="input_options">
+                <param name="input_mode" value="mixed_reads"/>
+                <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" />
+                <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />
+            </conditional>            
+            <output name="output_gtf" ftype="gtf">
+                <assert_contents>
+                    <has_text text="gi|251831106|ref|NC_012920.1|"/>
+                    <has_text text="StringTie version 2.2.1"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_in.cram
Binary file test-data/stringtie_in.cram has changed
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_merge_out1.gtf
--- a/test-data/stringtie_merge_out1.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_merge_out1.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_merge_out2.gtf
--- a/test-data/stringtie_merge_out2.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_merge_out2.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
 chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
 chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out1.gtf
--- a/test-data/stringtie_out1.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out1.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,5 +1,5 @@
 # stringtie /tmp/tmpgqe071sy/files/8/a/5/dataset_8a57065f-d332-4a26-8aa0-9d511312d8a6.dat -o /tmp/tmpgqe071sy/files/b/4/6/dataset_b46e6244-1199-4c7b-946c-111d2b3c98c7.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
+# StringTie version 2.2.1
 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 cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out10.gtf
--- a/test-data/stringtie_out10.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out10.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out11.gtf
--- a/test-data/stringtie_out11.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out11.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.815421";
 chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "4\.559259";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out12.gtf
--- a/test-data/stringtie_out12.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out12.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,5 +1,5 @@
-# StringTie version 2\.1\.7
-# stringtie short_sorted\.sam long_sorted\.sam -E 25 -o /[/.\-_A-Za-z0-9]+\.dat -p 2 -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# StringTie version 2\.2\.1
+# stringtie /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 chr16\tStringTie\texon\t784986\t786377\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "33\.698273";
 chr16\tStringTie\texon\t786827\t786928\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "24\.970589";
 chr16\tStringTie\texon\t787077\t787179\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "24\.747572";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out1_re.gtf
--- a/test-data/stringtie_out1_re.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out1_re.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out2.gtf
--- a/test-data/stringtie_out2.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out2.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,5 +1,5 @@
 # stringtie /tmp/tmpgqe071sy/files/c/e/6/dataset_ce6d871e-dc50-4710-8c21-385b1a4fcd2e.dat -o /tmp/tmpgqe071sy/files/e/8/2/dataset_e82c3d81-e413-4566-a538-1ef066ef2348.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
+# StringTie version 2.2.1
 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 cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out2_re.gtf
--- a/test-data/stringtie_out2_re.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out2_re.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out3.gtf
--- a/test-data/stringtie_out3.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out3.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,5 +1,5 @@
 # stringtie /tmp/tmpgqe071sy/files/8/6/e/dataset_86e4ed94-6458-4fd6-b8ae-dc5f7acd75ac.dat -o /tmp/tmpgqe071sy/files/5/7/7/dataset_57773891-c25a-4102-a817-04fa6e876cf3.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
+# StringTie version 2.2.1
 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 cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out3_re.gtf
--- a/test-data/stringtie_out3_re.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out3_re.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out4.gtf
--- a/test-data/stringtie_out4.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out4.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,5 +1,5 @@
 # stringtie /tmp/tmpgqe071sy/files/5/8/5/dataset_5851f244-d011-47e4-b6ac-bb6119b6497b.dat -o /tmp/tmpgqe071sy/files/d/a/6/dataset_da695139-3493-41cc-9409-8085cad59f40.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpgqe071sy/files/8/7/d/dataset_87d1ffdf-8041-4fc6-b9d7-7cd794f69cd8.dat
-# StringTie version 2.1.7
+# StringTie version 2.2.1
 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 cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out4_re.gtf
--- a/test-data/stringtie_out4_re.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out4_re.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95( -A /[-_/a-zA-Z0-9]+\.dat)?
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out5.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out6.gtf
--- a/test-data/stringtie_out6.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out6.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out8.gtf
--- a/test-data/stringtie_out8.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out8.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
diff -r cef79931dda5 -r 914cfcba0ec8 test-data/stringtie_out9.gtf
--- a/test-data/stringtie_out9.gtf	Wed Jul 27 09:28:15 2022 +0000
+++ b/test-data/stringtie_out9.gtf	Mon Oct 31 20:08:02 2022 +0000
@@ -1,4 +1,4 @@
-# StringTie version 2\.1\.7
+# StringTie version 2\.2\.1
 # stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";