| Previous changeset 9:1f23fc7df25c (2017-03-21) Next changeset 11:6e45b443ef1f (2017-06-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 |
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modified:
macros.xml stringtie.xml stringtie_merge.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_out7.gtf |
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added:
test-data/deseq2/gene_counts.tsv test-data/deseq2/legend.tsv test-data/deseq2/transcript_counts.tsv test-data/stringtie_out8.gtf |
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removed:
test-data/e2t.ctab test-data/e_data.ctab test-data/i2t.ctab test-data/i_data.ctab test-data/t_data.ctab tool_dependencies.xml |
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| diff -r 1f23fc7df25c -r c84d44519b2e macros.xml --- a/macros.xml Tue Mar 21 03:07:22 2017 -0400 +++ b/macros.xml Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2.3">stringtie</requirement> + <requirement type="package" version="1.3.3">stringtie</requirement> <yield/> </requirements> </xml> |
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| diff -r 1f23fc7df25c -r c84d44519b2e stringtie.xml --- a/stringtie.xml Tue Mar 21 03:07:22 2017 -0400 +++ b/stringtie.xml Tue Apr 04 12:58:27 2017 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="stringtie" name="StringTie" version="1.2.3">\n+<tool id="stringtie" name="StringTie" version="1.3.3">\n <description>transcript assembly and quantification</description>\n <macros>\n <import>macros.xml</import>\n@@ -8,28 +8,36 @@\n <expand macro="version_command" />\n <command>\n <![CDATA[\n+ mkdir -p ./special_de_output/sample1/ &&\n+ #if str($guide.use_guide) == \'yes\':\n+ ln -s \'$guide.guide_gff\' ./special_de_output/sample1/guide.gtf &&\n+ #end if\n+\n #if $input_bam.metadata.ftype == \'sam\':\n- samtools sort -@ \\${GALAXY_SLOTS:-1} "$input_bam" | stringtie\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_bam\' | stringtie\n #else\n- stringtie "$input_bam"\n+ stringtie \'$input_bam\'\n #end if\n+\n -o "$output_gtf"\n -p "\\${GALAXY_SLOTS:-1}"\n #if str($guide.use_guide) == \'yes\':\n- -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation\n- #if $guide.output_ballgown:\n- -b .\n+ -C \'$coverage\'\n+ -G \'$guide.guide_gff\'\n+ $guide.input_estimation\n+ #if $guide.special_outputs != \'no\':\n+ -b ./special_de_output/sample1/\n #end if\n #end if\n #if str($option_set.options) == \'advanced\':\n- -l "$option_set.name_prefix"\n- -f "$option_set.fraction"\n- -m "$option_set.min_tlen"\n- -a "$option_set.min_anchor_len"\n- -j "$option_set.min_anchor_cov"\n- -c "$option_set.min_bundle_cov"\n- -g "$option_set.bdist"\n- -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping\n+ -l \'$option_set.name_prefix\'\n+ -f \'$option_set.fraction\'\n+ -m \'$option_set.min_tlen\'\n+ -a \'$option_set.min_anchor_len\'\n+ -j \'$option_set.min_anchor_cov\'\n+ -c \'$option_set.min_bundle_cov\'\n+ -g \'$option_set.bdist\'\n+ -M \'$option_set.bundle_fraction\' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping\n #if $option_set.abundance_estimation:\n -A "$gene_abundance_estimation"\n #end if\n@@ -37,20 +45,63 @@\n -x "$option_set.omit_sequences"\n #end if\n #end if\n+\n+ #if str($guide.use_guide) == \'yes\':\n+ #if $guide.special_outputs.special_outputs_select == \'deseq2\':\n+ &&\n+ prepDE.py\n+ -i ./special_de_output/\n+ -g gene_cout_matrix.tsv\n+ -t transcripts_count_matrix.tsv\n+ -l $guide.special_outputs.read_length\n+ #if str($option_set.options) == \'advanced\':\n+ -s \'$option_set.name_prefix\'\n+ #end if\n+ #if $guide.special_outputs.clustering:\n+ -c\n+ --legend ./legend.tsv\n+\n+ &&\n+ sed -i.bak \'s/,/\\t/g\' ./legend.tsv\n+\n+ #end if\n+ &&\n+ sed -i.bak \'s/,/\\t/g\' transcripts_count_matrix.tsv\n+ &&\n+ sed -i.bak \'s/,/\\t/g\' gene_cout_matrix.tsv\n+ #end if\n+ #end if\n+\n ]]>\n </command>\n <inputs>\n <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />\n <conditional name="guide">\n <param label="Use GFF file to guide assembly" name="use_guide" type="select">\n- <option value="yes">Use GFF</option>\n- <option selected="True" value="no">Do not use GFF</option>\n+ <option value="yes">Use GFF/GTF</option>\n+ <option selected="True" value="no">Do not use GFF/GTF</option>\n </param>\n <when va'..b' <param name="options" value="advanced" />\n <param name="fraction" value="0.17" />\n@@ -132,35 +208,50 @@\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n <param name="use_guide" value="yes" />\n- <param name="output_ballgown" value="yes" />\n+ <param name="special_outputs_select" value="ballgown" />\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="default" />\n- <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />\n- <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />\n- <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />\n- <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />\n- <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />\n+ <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />\n+ <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />\n+ <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />\n+ <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />\n+ <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />\n <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />\n </test>\n <test>\n <param ftype="bam" name="input_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="guide_gff" value="stringtie_in.gtf" />\n+ <param name="options" value="default" />\n+ <param name="clustering" value="True" />\n+ <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" />\n+ <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" />\n+ <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" />\n+ <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n+ <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />\n+ </test>\n+ <test>\n+ <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n+ <param name="use_guide" value="yes" />\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="advanced" />\n <param name="fraction" value="0.17" />\n <param name="abundance_estimation" value="True" />\n <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n- <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />\n+ <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />\n </test>\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n <param name="use_guide" value="yes" />\n+ <param name="special_outputs_select" value="no" />\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="advanced" />\n <param name="fraction" value="0.15" />\n <param name="c" value="test_chromosome" />\n- <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n+ <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n </test>\n </tests>\n <help>\n' |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e stringtie_merge.xml --- a/stringtie_merge.xml Tue Mar 21 03:07:22 2017 -0400 +++ b/stringtie_merge.xml Tue Apr 04 12:58:27 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="stringtie_merge" name="StringTie" version="0.1.0"> +<tool id="stringtie_merge" name="StringTie" version="1.3.3"> <description>merge transcripts</description> <macros> <import>macros.xml</import> |
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| diff -r 1f23fc7df25c -r c84d44519b2e test-data/ballgown/t_data.ctab --- a/test-data/ballgown/t_data.ctab Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/ballgown/t_data.ctab Tue Apr 04 12:58:27 2017 -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 . 44.724823 3276543.750000 +1 test_chromosome + 53 550 CUFF.1.1 3 298 CUFF.1 . 44.070122 3228580.250000 |
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| diff -r 1f23fc7df25c -r c84d44519b2e test-data/deseq2/gene_counts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq2/gene_counts.tsv Tue Apr 04 12:58:27 2017 -0400 |
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| @@ -0,0 +1,2 @@ + sample1 +CUFF.1 574 |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/deseq2/transcript_counts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq2/transcript_counts.tsv Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ + sample1 +CUFF.1.1 574 |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_merge_out1.gtf --- a/test-data/stringtie_merge_out1.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_merge_out1.gtf Tue Apr 04 12:58:27 2017 -0400 |
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| @@ -1,5 +1,5 @@ -# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_5.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_6.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_1.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_2.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_3.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_4.dat -# StringTie version 1.2.3 +# 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 1.3.3 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"; |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_merge_out2.gtf --- a/test-data/stringtie_merge_out2.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_merge_out2.gtf Tue Apr 04 12:58:27 2017 -0400 |
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| b'@@ -1,5 +1,5 @@\n-# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_9.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_10.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_7.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_8.dat\n-# StringTie version 1.2.3\n+# 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\n+# StringTie version 1.3.3\n chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; \n chr1\tStringTie\texon\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; \n chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; \n@@ -47,54 +47,54 @@\n chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t.\t.\tgene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; \n chr1\tStringTie\texon\t3450907\t3451109\t1000\t.\t.\tgene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; \n chr1\tmm9_refFlat\ttranscript\t4334224\t4350473\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";\n-chr1\tmm9_refFlat\texon\t4334224\t4340172\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; ref_gene_id "Rp1";\n-chr1\tmm9_refFlat\texon\t4341991\t4342162\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1";\n-chr1\tmm9_refFlat\texon\t4342283\t4342918\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1";\n-chr1\tmm9_refFlat\texon\t4350281\t4350473\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1";\n+chr1\tmm9_refFlat\texon\t4334224\t4340172\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4341991\t4342162\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4342283\t4342918\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4350281\t4350473\t.\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "4";\n chr1\tmm9_refFlat\ttranscript\t4481009\t4486494\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";\n-chr1\tmm9_refFlat\texon\t4481009\t4482749\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; ref_gene_id "Sox17";\n-chr1\tmm9_refFlat\texon\t4483181\t4483547\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17";\n-chr1\tmm9_refFlat\texon\t4483853\t4483944\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17";\n-chr1\tmm9_refFlat\texon\t4485217\t4486023\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17";\n-chr1\tmm9_refFlat\texon\t4486372\t4486494\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17";\n+chr1\tmm9_refFlat\texon\t4481009\t4482749\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4483181\t4483547\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4483853\t4483944\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4485217\t4486023\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4486372\t4486494\t.\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "5";\n chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";\n-chr1\tmm9_refFlat\texon\t4763279\t4766882\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; ref_gene_id "Mrpl15";\n-chr1\tmm9_refFlat\texon\t4767606\t4767729\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15";\n-chr1\tmm9_refFlat\texon\t4772649\t4772814\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15";\n-chr1\tmm9_refFlat\texon\t4774032\t4774186\t.\t-\t.\tgene_id "M'..b'lat\texon\t4835044\t4836816\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4797974\t4798063\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4798536\t4798567\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4818665\t4818730\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4820349\t4820396\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4822392\t4822462\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";\n+chr1\tmm9_refFlat\texon\t4827082\t4827155\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";\n+chr1\tmm9_refFlat\texon\t4829468\t4829569\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";\n+chr1\tmm9_refFlat\texon\t4831037\t4831213\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";\n+chr1\tmm9_refFlat\texon\t4835044\t4836816\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";\n chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";\n chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4868108\t4868213\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4876825\t4876912\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4879538\t4879683\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4880821\t4880877\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4881996\t4882150\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4883498\t4883644\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4885015\t4885086\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1";\n-chr1\tmm9_refFlat\texon\t4886437\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4868108\t4868213\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4876825\t4876912\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4879538\t4879683\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";\n+chr1\tmm9_refFlat\texon\t4880821\t4880877\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";\n+chr1\tmm9_refFlat\texon\t4881996\t4882150\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";\n+chr1\tmm9_refFlat\texon\t4883498\t4883644\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";\n+chr1\tmm9_refFlat\texon\t4885015\t4885086\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";\n+chr1\tmm9_refFlat\texon\t4886437\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";\n' |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out1.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_2.dat -p 1 -# StringTie version 1.2.3 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; +# stringtie /tmp/tmpJfKWNy/files/000/dataset_1.dat -o /tmp/tmpJfKWNy/files/000/dataset_2.dat -p 1 +# StringTie version 1.3.3 +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"; +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"; |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out2.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_9.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.2.3 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; +# 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 1.3.3 +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"; +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"; |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out3.gtf --- a/test-data/stringtie_out3.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out3.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_16.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_18.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_20.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_17.dat -# StringTie version 1.2.3 -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 "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; -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 "49.011967"; -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 "51.382565"; -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 "21.090000"; +# 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 1.3.3 +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 "44.070122"; FPKM "3228580.250000"; TPM "962398.937500"; +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 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out4.gtf --- a/test-data/stringtie_out4.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out4.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_3.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_5.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_2.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_4.dat -# StringTie version 1.2.3 -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 "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; -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 "49.011967"; -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 "51.382565"; -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 "21.090000"; +# 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 1.3.3 +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 "44.070122"; FPKM "3228580.250000"; TPM "962398.937500"; +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 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out5.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_25.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_27.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_29.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_26.dat -B -# StringTie version 1.2.3 -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 "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; -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 "49.011967"; -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 "51.382565"; -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 "21.090000"; +# 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 1.3.3 +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 "44.070122"; FPKM "3228580.250000"; TPM "962398.937500"; +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 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out6.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,3 +1,6 @@ -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 +# stringtie /tmp/tmpJfKWNy/files/000/dataset_22.dat -o /tmp/tmpJfKWNy/files/000/dataset_24.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_25.dat -G /tmp/tmpJfKWNy/files/000/dataset_23.dat -e -b ./special_de_output/sample1/ +# StringTie version 1.3.3 +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"; +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"; |
| b |
| diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out7.gtf --- a/test-data/stringtie_out7.gtf Tue Mar 21 03:07:22 2017 -0400 +++ b/test-data/stringtie_out7.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -1,6 +1,3 @@ -# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_39.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_41.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_42.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_40.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.2.3 -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 "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; -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 "49.011967"; -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 "51.382565"; -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 "21.090000"; +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 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out8.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out8.gtf Tue Apr 04 12:58:27 2017 -0400 |
| b |
| @@ -0,0 +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 1.3.3 +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 "44.070122"; FPKM "3228580.250000"; TPM "962398.937500"; +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 1f23fc7df25c -r c84d44519b2e tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 21 03:07:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="stringtie" version="1.2.3"> - <repository changeset_revision="ee804c6f3b97" name="package_stringtie_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |