# HG changeset patch # User iuc # Date 1582672067 18000 # Node ID 1ebd14235b927401d74ad7d7aa7fbb9cd2d95212 # Parent eba36e001f455460244a252da43a4cd336bc14b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit afa107c23e8eb889f0ed3469e2c897447be6bbf8" diff -r eba36e001f45 -r 1ebd14235b92 macros.xml --- 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 @@ - 1.3.6 + 2.1.1 stringtie @@ -14,6 +14,7 @@ + 10.1186/s13059-019-1910-1 10.1038/nbt.3122 diff -r eba36e001f45 -r 1ebd14235b92 stringtie.xml --- 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 @@ ]]> + diff -r eba36e001f45 -r 1ebd14235b92 test-data/ballgown/t_data.ctab --- 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 diff -r eba36e001f45 -r 1ebd14235b92 test-data/gene_counts_edger.tsv --- 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 diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_merge_out1.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_merge_out2.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out1.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out2.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out3.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out4.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out5.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out6.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out7.tsv --- 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 diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out8.gtf --- 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"; diff -r eba36e001f45 -r 1ebd14235b92 test-data/stringtie_out_coverage.gtf --- 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 diff -r eba36e001f45 -r 1ebd14235b92 test-data/transcript_counts_edger.tsv --- 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