| Previous changeset 15:dd4df992d93d (2018-07-24) Next changeset 17:1ebd14235b92 (2020-02-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 |
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modified:
macros.xml stringtie.xml test-data/ballgown/t_data.ctab 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_out8.gtf test-data/stringtie_out_coverage.gtf |
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added:
test-data/stringtie_out7.tsv |
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removed:
test-data/._stringtie_in1.bam test-data/._stringtie_out2.gtf test-data/stringtie_out7.gtf |
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| diff -r dd4df992d93d -r eba36e001f45 macros.xml --- a/macros.xml Tue Jul 24 10:23:37 2018 -0400 +++ b/macros.xml Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.3.4</token> + <token name="@TOOL_VERSION@">1.3.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement> |
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| diff -r dd4df992d93d -r eba36e001f45 stringtie.xml --- a/stringtie.xml Tue Jul 24 10:23:37 2018 -0400 +++ b/stringtie.xml Fri May 03 11:05:13 2019 -0400 |
| [ |
| b'@@ -112,14 +112,14 @@\n <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"/>\n <param name="rna_strandness" type="select" label="Specify strand information"\n 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">\n- <option value="" selected="True">Unstranded</option>\n+ <option value="" selected="true">Unstranded</option>\n <option value="--fr">Forward (FR)</option>\n <option value="--rf">Reverse (RF)</option>\n </param>\n <conditional name="guide">\n <param name="use_guide" argument="-G" type="select" label="Use a reference file to guide assembly?" help="Use the reference annotation file (in GTF or GFF3 format) to guide the assembly process. The output will include expressed reference transcripts as well as any novel transcripts that are assembled. This option is required by option -e (Use Reference transcripts only), see below.">\n <option value="yes">Use reference GTF/GFF3</option>\n- <option value="no" selected="True" >Do not use reference GTF/GFF3</option>\n+ <option value="no" selected="true" >Do not use reference GTF/GFF3</option>\n </param>\n <when value="no" />\n <when value="yes">\n@@ -140,12 +140,12 @@\n <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />\n </when>\n </conditional>\n- <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/>\n+ <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/>\n <conditional name="special_outputs">\n <param name="special_outputs_select" type="select" label="Output files for differential expression?" help="Select to output additional files that can be used with Ballgown or DESeq2/edgeR. See Help section below for more information">\n <option value="ballgown">Ballgown</option>\n <option value="deseq2">DESeq2/edgeR/limma-voom</option>\n- <option value="no" selected="True">No additional output</option>\n+ <option value="no" selected="true">No additional output</option>\n </param>\n <when value="ballgown" />\n <when value="deseq2">\n@@ -164,11 +164,11 @@\n </when>\n <when value="no" />\n </conditional>\n- <param name="coverage_file" argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="False'..b'anscripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript\'s start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />\n- <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Disable multi-mapping correction" help="Default: No"/>\n+ <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript\'s start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />\n+ <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>\n </section>\n </inputs>\n <outputs>\n <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />\n- <data name="gene_abundance_estimation" format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates">\n+ <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">\n <filter>adv[\'abundance_estimation\']</filter>\n </data>\n <data name="coverage" format="gtf" label="${tool.name} on ${on_string}: Coverage">\n@@ -260,7 +260,7 @@\n <param name="guide_gff_select" value="history" />\n <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />\n <param name="special_outputs_select" value="ballgown" />\n- <param name="coverage_file" value="True" />\n+ <param name="coverage_file" value="true" />\n <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />\n <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />\n <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />\n@@ -274,11 +274,11 @@\n <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />\n <param name="use_guide" value="yes" />\n <param name="special_outputs_select" value="deseq2" />\n- <param name="input_estimation" value="True" />\n+ <param name="input_estimation" value="true" />\n <param name="guide_gff_select" value="history" />\n <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />\n- <param name="coverage_file" value="True" />\n- <param name="clustering" value="True" />\n+ <param name="coverage_file" value="true" />\n+ <param name="clustering" value="true" />\n <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />\n <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />\n <output name="legend" file="legend.tsv" ftype="tabular" />\n@@ -292,9 +292,9 @@\n <param name="guide_gff_select" value="history" />\n <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />\n <param name="fraction" value="0.17" />\n- <param name="abundance_estimation" value="True" />\n+ <param name="abundance_estimation" value="true" />\n <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />\n- <output name="gene_abundance_estimation" file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" />\n+ <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />\n </test>\n <!--Ensure another fraction value works -->\n <test expect_num_outputs="1">\n' |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/._stringtie_in1.bam |
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| Binary file test-data/._stringtie_in1.bam has changed |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/._stringtie_out2.gtf |
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| Binary file test-data/._stringtie_out2.gtf has changed |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/ballgown/t_data.ctab --- a/test-data/ballgown/t_data.ctab Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/ballgown/t_data.ctab Fri May 03 11:05:13 2019 -0400 |
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| @@ -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 3228580.250000 +1 test_chromosome + 53 550 CUFF.1.1 3 298 CUFF.1 . 44.070122 3228580.366300 |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_merge_out1.gtf --- a/test-data/stringtie_merge_out1.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_merge_out1.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,5 +1,5 @@ -# stringtie --merge -p 1 -G /tmp/tmpJfKWNy/files/000/dataset_42.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpJfKWNy/files/000/dataset_43.dat /tmp/tmpJfKWNy/files/000/dataset_38.dat /tmp/tmpJfKWNy/files/000/dataset_39.dat /tmp/tmpJfKWNy/files/000/dataset_40.dat /tmp/tmpJfKWNy/files/000/dataset_41.dat -# StringTie version 1.3.4d +# 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 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_merge_out2.gtf --- a/test-data/stringtie_merge_out2.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_merge_out2.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,5 +1,5 @@ -# stringtie --merge -p 1 -G /tmp/tmpJfKWNy/files/000/dataset_46.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpJfKWNy/files/000/dataset_47.dat /tmp/tmpJfKWNy/files/000/dataset_44.dat /tmp/tmpJfKWNy/files/000/dataset_45.dat -# StringTie version 1.3.4d +# 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 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out1.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_1.dat -o /tmp/tmpJfKWNy/files/000/dataset_2.dat -p 1 -# StringTie version 1.3.4d -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227877.000000"; TPM "962189.250000"; +# 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out2.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_3.dat -o /tmp/tmpJfKWNy/files/000/dataset_4.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.3.4d -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227877.000000"; TPM "962189.250000"; +# 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out3.gtf --- a/test-data/stringtie_out3.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out3.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_5.dat -o /tmp/tmpJfKWNy/files/000/dataset_7.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_8.dat -G /tmp/tmpJfKWNy/files/000/dataset_6.dat -b ./special_de_output/sample1/ -# StringTie version 1.3.4d -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 "3228580.250000"; TPM "962398.937500"; +# 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out4.gtf --- a/test-data/stringtie_out4.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out4.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_28.dat -o /tmp/tmpJfKWNy/files/000/dataset_30.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_32.dat -G /tmp/tmpJfKWNy/files/000/dataset_29.dat -b ./special_de_output/sample1/ -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpJfKWNy/files/000/dataset_31.dat -# StringTie version 1.3.4d -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 "3228580.250000"; TPM "962398.937500"; +# 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out5.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_13.dat -o /tmp/tmpJfKWNy/files/000/dataset_15.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_16.dat -G /tmp/tmpJfKWNy/files/000/dataset_14.dat -b ./special_de_output/sample1/ -# StringTie version 1.3.4d -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 "3228580.250000"; TPM "962398.937500"; +# 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"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out6.gtf Fri May 03 11:05:13 2019 -0400 |
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| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpSoPTYX/files/000/dataset_1.dat -o /tmp/tmpSoPTYX/files/000/dataset_3.dat -p 1 -G guide.gff -C /tmp/tmpSoPTYX/files/000/dataset_4.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 1.3.4d -test_chromosome StringTie transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.795296"; FPKM "3354966.750000"; TPM "1000000.000000"; +# 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"; test_chromosome StringTie exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000"; |
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| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out7.gtf --- a/test-data/stringtie_out7.gtf Tue Jul 24 10:23:37 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM -CUFF.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500 -STRG.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500 |
| b |
| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out7.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out7.tsv Fri May 03 11:05:13 2019 -0400 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out8.gtf --- a/test-data/stringtie_out8.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out8.gtf Fri May 03 11:05:13 2019 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_34.dat -o /tmp/tmpJfKWNy/files/000/dataset_36.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_37.dat -G /tmp/tmpJfKWNy/files/000/dataset_35.dat -b ./special_de_output/sample1/ -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.3.4d -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 "3228580.250000"; TPM "962398.937500"; +# 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"; |
| b |
| diff -r dd4df992d93d -r eba36e001f45 test-data/stringtie_out_coverage.gtf --- a/test-data/stringtie_out_coverage.gtf Tue Jul 24 10:23:37 2018 -0400 +++ b/test-data/stringtie_out_coverage.gtf Fri May 03 11:05:13 2019 -0400 |
| b |
| @@ -1,4 +1,4 @@ -test_chromosome Cufflinks transcript 53 550 1000.00 + . ID=CUFF.1.1;geneID=CUFF.1 -test_chromosome Cufflinks exon 53 250 1000.00 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 351 400 1000.00 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 501 550 1000.00 + . Parent=CUFF.1.1 +test_chromosome Cufflinks transcript 53 550 1000 + . ID=CUFF.1.1;geneID=CUFF.1 +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 |