Mercurial > repos > iuc > stringtie

changeset 17:1ebd14235b92 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit afa107c23e8eb889f0ed3469e2c897447be6bbf8"
author iuc
date Tue, 25 Feb 2020 18:07:47 -0500
parents eba36e001f45
children 258d696dbd7e
files macros.xml stringtie.xml test-data/ballgown/t_data.ctab test-data/gene_counts_edger.tsv test-data/stringtie_merge_out1.gtf test-data/stringtie_merge_out2.gtf test-data/stringtie_out1.gtf test-data/stringtie_out2.gtf test-data/stringtie_out3.gtf test-data/stringtie_out4.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out7.tsv test-data/stringtie_out8.gtf test-data/stringtie_out_coverage.gtf test-data/transcript_counts_edger.tsv
diffstat 16 files changed, 57 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri May 03 11:05:13 2019 -0400
+++ b/macros.xml	Tue Feb 25 18:07:47 2020 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.6</token>
+    <token name="@TOOL_VERSION@">2.1.1</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
@@ -14,6 +14,7 @@
     </xml>
     <xml name="citations">
         <citations>
+            <citation type="doi">10.1186/s13059-019-1910-1</citation>
             <citation type="doi">10.1038/nbt.3122</citation>
             <yield />
         </citations>
--- a/stringtie.xml	Fri May 03 11:05:13 2019 -0400
+++ b/stringtie.xml	Tue Feb 25 18:07:47 2020 -0500
@@ -21,11 +21,13 @@
 #end if
 
 #if $input_bam.metadata.ftype == 'sam':
-    samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
+    samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' -T "\${TMPDIR:-.}" | stringtie
 #else
     stringtie '$input_bam'
 #end if
 
+$long_reads
+
 -o '$output_gtf'
 -p "\${GALAXY_SLOTS:-1}"
 
@@ -110,6 +112,7 @@
     ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>
+        <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Input contains long reads?" help="Select if the input contains long error-prone reads, e.g. from Oxford Nanopore or PacBio sequencing."/>
         <param name="rna_strandness" type="select" label="Specify strand information"
             help="Select 'Forward (FR)' if your reads are from a forward-stranded library, 'Reverse (RF)' if your reads are from a reverse-stranded library, or 'Unstranded' if your reads are not from a stranded library. See Help section below for more information. Default: Unstranded">
                 <option value="" selected="true">Unstranded</option>
--- a/test-data/ballgown/t_data.ctab	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/ballgown/t_data.ctab	Tue Feb 25 18:07:47 2020 -0500
@@ -1,2 +1,2 @@
 t_id	chr	strand	start	end	t_name	num_exons	length	gene_id	gene_name	cov	FPKM
-1	test_chromosome	+	53	550	CUFF.1.1	3	298	CUFF.1	.	44.070122	3228580.366300
+1	test_chromosome	+	53	550	CUFF.1.1	3	298	CUFF.1	.	45.241611	3314403.750000
--- a/test-data/gene_counts_edger.tsv	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/gene_counts_edger.tsv	Tue Feb 25 18:07:47 2020 -0500
@@ -1,2 +1,2 @@
 gene_id	stringtie_in1_bam
-CUFF.1	182
+CUFF.1	180
--- a/test-data/stringtie_merge_out1.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_merge_out1.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /tmp/tmpcy98bsa4/files/000/dataset_40.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpcy98bsa4/files/000/dataset_41.dat /tmp/tmpcy98bsa4/files/000/dataset_36.dat /tmp/tmpcy98bsa4/files/000/dataset_37.dat /tmp/tmpcy98bsa4/files/000/dataset_38.dat /tmp/tmpcy98bsa4/files/000/dataset_39.dat
-# StringTie version 1.3.6
+# stringtie --merge -p 1 -G /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/0/e/dataset_10e968ed-4fcb-4799-864f-4a845aefd7c6.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/d/4/7/dataset_d47ec42c-d204-4b1a-b863-c54d1f0f8aba.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/4/9/dataset_b496e60c-ee18-4c69-99eb-70f9445725f5.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/4/b/a/dataset_4bac764c-1632-4ba8-bf86-dbeda729238e.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/3/3/dataset_933d8dbf-024c-4bad-b90f-05f847a7406f.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/f/a/2/dataset_fa27d83d-cfd4-4910-abdb-b83cf2668486.dat
+# StringTie version 2.1.1
 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"; 
--- a/test-data/stringtie_merge_out2.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_merge_out2.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /tmp/tmpcy98bsa4/files/000/dataset_44.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpcy98bsa4/files/000/dataset_45.dat /tmp/tmpcy98bsa4/files/000/dataset_42.dat /tmp/tmpcy98bsa4/files/000/dataset_43.dat
-# StringTie version 1.3.6
+# stringtie --merge -p 1 -G /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/3/7/dataset_e372bcb2-3b02-4fa2-8e9a-e5f9fb2ddd1a.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/d/4/dataset_bd4ebf5e-a629-4b3e-ab7c-bba17f0e7651.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/c/4/8/dataset_c480ac0d-da44-4477-a115-43d849c4e0fb.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/b/a/dataset_1ba088e7-52b5-4783-a7a5-b023862e36e2.dat
+# StringTie version 2.1.1
 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"; 
--- a/test-data/stringtie_out1.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out1.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_1.dat -o /tmp/tmpcy98bsa4/files/000/dataset_2.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.3.6
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227876.923077"; TPM "962189.281155";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.012157";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/c/7/a/dataset_c7af8b5d-2e42-4fea-b8d6-7fad0726e917.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/3/5/7/dataset_357301ba-858d-44ea-9ead-8160748e75fc.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000";
--- a/test-data/stringtie_out2.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out2.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_3.dat -o /tmp/tmpcy98bsa4/files/000/dataset_4.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.3.6
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227876.923077"; TPM "962189.281155";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.012157";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/0/b/d/dataset_0bdef9bb-4df2-495e-96e5-172272d8d091.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/a/2/dataset_ea28bbaf-b541-4047-a923-87fad9958466.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000";
--- a/test-data/stringtie_out3.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out3.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_5.dat -o /tmp/tmpcy98bsa4/files/000/dataset_7.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 1.3.6
-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 "44.070122"; FPKM "3228580.366300"; TPM "962398.968682";
-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 "48.005386";
-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 "51.452003";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/3/8/4/dataset_384eded7-d60c-439d-be66-1b9963159f17.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/4/8/dataset_b482f931-c707-4535-b3e0-500c8d8e871b.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 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
--- a/test-data/stringtie_out4.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out4.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_27.dat -o /tmp/tmpcy98bsa4/files/000/dataset_29.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/tmpcy98bsa4/files/000/dataset_30.dat
-# StringTie version 1.3.6
-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 "44.070122"; FPKM "3228580.366300"; TPM "962398.968682";
-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 "48.005386";
-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 "51.452003";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/0/6/f/dataset_06f2148a-c2bc-4d89-a2d7-e3e1a8afa1c6.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/1/c/dataset_11c0064f-b50b-4810-b856-1b16030c6a6b.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
+# StringTie version 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
--- a/test-data/stringtie_out5.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out5.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_11.dat -o /tmp/tmpcy98bsa4/files/000/dataset_13.dat -p 1 -G guide.gff -C /tmp/tmpcy98bsa4/files/000/dataset_14.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.3.6
-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 "44.070122"; FPKM "3228580.366300"; TPM "962398.968682";
-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 "48.005386";
-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 "51.452003";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/7/d/b/dataset_7db84341-79f0-4976-93ae-077d5bc204fe.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/c/0/dataset_9c0876b6-2850-4467-9983-65e7e1e60147.dat -p 1 -G guide.gff -C /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/7/0/f/dataset_70fc75f5-d3a9-4f0e-b3e5-ae748f5ea145.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
--- a/test-data/stringtie_out6.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out6.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_20.dat -o /tmp/tmpcy98bsa4/files/000/dataset_22.dat -p 1 -G guide.gff -C /tmp/tmpcy98bsa4/files/000/dataset_23.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.3.6
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.795296"; FPKM "3354966.739927"; TPM "1000000.006216";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.777779";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "54.160004";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/7/9/dataset_979811c5-c516-4209-bd38-3677704d573f.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/2/5/6/dataset_256d374e-00c0-40ba-979b-0a65edd889e2.dat -p 1 -G guide.gff -C /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/4/f/dataset_e4fa5924-6856-4ba9-97d7-99aa2b3cff62.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 2.1.1
+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 "53.000000";
 test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000";
--- a/test-data/stringtie_out7.tsv	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out7.tsv	Tue Feb 25 18:07:47 2020 -0500
@@ -1,3 +1,3 @@
 Gene ID	Gene Name	Reference	Strand	Start	End	Coverage	FPKM	TPM
-CUFF.1	-	test_chromosome	+	53	550	45.791946	3354721.318681	999999.991022
-STRG.1	-	test_chromosome	+	53	550	45.791946	3354721.318681	999999.991022
+CUFF.1	-	test_chromosome	+	53	550	45.241611	3314403.750000	1000000.000000
+STRG.1	-	test_chromosome	+	53	550	45.241611	3314403.750000	1000000.000000
--- a/test-data/stringtie_out8.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out8.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpcy98bsa4/files/000/dataset_34.dat -o /tmp/tmpcy98bsa4/files/000/dataset_35.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 1.3.6
-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 "44.070122"; FPKM "3228580.366300"; TPM "962398.968682";
-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 "48.005386";
-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 "51.452003";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
+# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmp6o9_xiyd/files/4/4/4/dataset_444ed4bd-2499-449b-b9d9-22d1704cea80.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmp6o9_xiyd/files/d/5/e/dataset_d5e42756-7a1f-4cdc-8cc7-7b9cb62ffb3a.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 2.1.1
+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 "53.000000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
--- a/test-data/stringtie_out_coverage.gtf	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/stringtie_out_coverage.gtf	Tue Feb 25 18:07:47 2020 -0500
@@ -1,4 +1,4 @@
-test_chromosome	Cufflinks	transcript	53	550	1000	+	.	ID=CUFF.1.1;geneID=CUFF.1
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	ID=CUFF.1.1;geneID=CUFF.1;coverage=60.97
 test_chromosome	Cufflinks	exon	53	250	1000	+	.	Parent=CUFF.1.1
 test_chromosome	Cufflinks	exon	351	400	1000	+	.	Parent=CUFF.1.1
 test_chromosome	Cufflinks	exon	501	550	1000	+	.	Parent=CUFF.1.1
--- a/test-data/transcript_counts_edger.tsv	Fri May 03 11:05:13 2019 -0400
+++ b/test-data/transcript_counts_edger.tsv	Tue Feb 25 18:07:47 2020 -0500
@@ -1,2 +1,2 @@
 transcript_id	stringtie_in1_bam
-CUFF.1.1	182
+CUFF.1.1	180