| Previous changeset 0:62d212192002 (2014-07-03) Next changeset 2:520e0988ec1c (2015-05-14) |
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Commit message:
Uploaded updated tool wrapper for stringtie 1.0.1 |
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modified:
stringtie.xml test-data/stringtie_in1.bam test-data/stringtie_out1.gtf test-data/stringtie_out2.gtf tool_dependencies.xml |
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added:
test-data/ballgown/e2t.ctab test-data/ballgown/e_data.ctab test-data/ballgown/i2t.ctab test-data/ballgown/i_data.ctab test-data/ballgown/t_data.ctab test-data/stringtie_in.gtf test-data/stringtie_out3.gtf test-data/stringtie_out4.gtf test-data/stringtie_out5.gtf test-data/stringtie_out_coverage.gtf |
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removed:
test-data/._stringtie_in1.bam test-data/._stringtie_out2.gtf |
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| diff -r 62d212192002 -r 9f80c71f1779 stringtie.xml --- a/stringtie.xml Thu Jul 03 18:38:02 2014 -0400 +++ b/stringtie.xml Thu Mar 05 11:41:12 2015 -0500 |
| [ |
| b'@@ -1,19 +1,20 @@\n-<?xml version="1.0"?>\n-<tool name="StringTie" id="stringtie" version="1.0.0">\n+<tool id="stringtie" name="StringTie" version="1.0.1">\n <description>RNA-Seq assembler</description>\n <requirements>\n- <requirement type="package" version="0.97">stringtie</requirement>\n+ <requirement type="package" version="1.0.1">stringtie</requirement>\n </requirements>\n- <command>\n-<![CDATA[\n+ <command><![CDATA[\n stringtie "$input_bam"\n -o "$output_gtf"\n -p "\\${GALAXY_SLOTS:-1}"\n #if str($guide.use_guide) == \'yes\':\n- -G "$guide.guide_gff" $guide.input_estimation\n- -C "$coverage"\n+ -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation\n+ #if str($guide.output_ballgown) == \'-b\':\n+ $guide.output_ballgown `pwd`\n+ #end if\n #end if\n #if str($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@@ -26,92 +27,142 @@\n ]]>\n </command>\n <inputs>\n- <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />\n+ <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />\n <conditional name="guide">\n- <param name="use_guide" type="select" label="Use GFF file to guide assembly">\n+ <param label="Use GFF file to guide assembly" name="use_guide" type="select">\n <option value="yes">Use GFF</option>\n- <option value="no" selected="True">Do not use GFF</option>\n+ <option selected="True" value="no">Do not use GFF</option>\n </param>\n <when value="no" />\n <when value="yes">\n- <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" />\n- <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" />\n+ <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />\n+ <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />\n+ <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />\n </when>\n </conditional>\n <conditional name="option_set">\n- <param name="options" type="select" label="Options">\n- <option value="default" selected="True">Use defaults</option>\n+ <param label="Options" name="options" type="select">\n+ <option selected="True" value="default">Use defaults</option>\n <option value="advanced">Specify advanced options</option>\n </param>\n <when value="default" />\n <when value="advanced">\n- <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />\n- <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />\n- <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" />\n- <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />\n- <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />\n- <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />\n- <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" />\n- <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads '..b' <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" name="output_gtf" />\n+ <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />\n </test>\n </tests>\n <help>\n <![CDATA[\n-StringTie v0.97 usage::\n-\n- stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>]\n- [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]\n- [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]\n-\n- Assemble RNA-Seq alignments into potential transcripts.\n+StringTie v1.0.1 usage:\n+ stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]\n+ [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]\n+ [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]\n+ {-B | -b <dir_path>} [-e]\n \n- Options:\n- -G reference annotation to use for guiding the assembly process (GTF/GFF3)\n- -l name prefix for output transcripts (default: STRG)\n- -f minimum isoform fraction (default: 0.15)\n- -m minimum assembled transcript length to report (default 200bp)\n- -o output file with the assembled transcripts (default: stdout)\n- -a minimum anchor length for junctions (default: 10)\n- -j minimum junction coverage (default: 1)\n- -t disable trimming of predicted transcripts based on coverage (default: trimming enabled)\n- -c minimum bundle reads per bp coverage to consider for assembly (default: 2)\n- -s coverage saturation threshold; further read alignments will be\n- ignored in a region where a local coverage depth of <maxcov>\n- is reached (default: 1,000,000);\n- -v verbose (log bundle processing details)\n- -e abundance estimation only of input transcripts (for -G option)\n- -g gap between read mappings triggering a new bundle (default: 50)\n- -S more sensitive run (default: no)\n- -C output file with all transcripts in reference that are fully\n- covered by reads\n- -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)\n- -p number of threads (CPUs) to use (default: 1)\n-\n-]]>\n-</help>\n-</tool>\n\\ No newline at end of file\n+Assemble RNA-Seq alignments into potential transcripts.\n+ \n+ Options:\n+ -G reference annotation to use for guiding the assembly process (GTF/GFF3)\n+ -l name prefix for output transcripts (default: STRG)\n+ -f minimum isoform fraction (default: 0.1)\n+ -m minimum assembled transcript length to report (default 200bp)\n+ -o output path/file name for the assembled transcripts GTF (default: stdout)\n+ -a minimum anchor length for junctions (default: 10)\n+ -j minimum junction coverage (default: 1)\n+ -t disable trimming of predicted transcripts based on coverage\n+ (default: coverage trimming is enabled)\n+ -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)\n+ -s coverage saturation threshold; further read alignments will be\n+ ignored in a region where a local coverage depth of <maxcov> \n+ is reached (default: 1,000,000);\n+ -v verbose (log bundle processing details)\n+ -g gap between read mappings triggering a new bundle (default: 50)\n+ -C output file with reference transcripts that are covered by reads\n+ -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)\n+ -p number of threads (CPUs) to use (default: 1)\n+ -B enable output of Ballgown table files which will be created in the\n+ same directory as the output GTF (requires -G, -o recommended)\n+ -b enable output of Ballgown table files but these files will be \n+ created under the directory path given as <dir_path>\n+ -e only estimates the abundance of given reference transcripts (requires -G)\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">doi:10.1038/nbt.3122</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/._stringtie_in1.bam |
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| Binary file test-data/._stringtie_in1.bam has changed |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/._stringtie_out2.gtf |
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| Binary file test-data/._stringtie_out2.gtf has changed |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/e2t.ctab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ballgown/e2t.ctab Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +1,4 @@ +e_id t_id +1 1 +2 1 +3 1 |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/e_data.ctab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ballgown/e_data.ctab Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +1,4 @@ +e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd +1 test_chromosome + 53 250 154 154 154.00 49.7778 22.0747 49.7778 22.0747 +2 test_chromosome + 351 400 73 73 73.00 54.1600 6.1753 54.1600 6.1753 +3 test_chromosome + 501 550 38 38 38.00 21.6400 12.4350 21.6400 12.4350 |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/i2t.ctab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ballgown/i2t.ctab Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +1,3 @@ +i_id t_id +1 1 +2 1 |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/i_data.ctab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ballgown/i_data.ctab Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +1,3 @@ +i_id chr strand start end rcount ucount mrcount +1 test_chromosome + 251 350 49 49 49.00 +2 test_chromosome + 401 500 38 38 38.00 |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/t_data.ctab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ballgown/t_data.ctab Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +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 |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_in.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_in.gtf Thu Mar 05 11:41:12 2015 -0500 |
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| @@ -0,0 +1,4 @@ +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_in1.bam |
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| Binary file test-data/stringtie_in1.bam has changed |
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| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Thu Jul 03 18:38:02 2014 -0400 +++ b/test-data/stringtie_out1.gtf Thu Mar 05 11:41:12 2015 -0500 |
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| b'@@ -1,154 +1,4 @@\n-chr19\tStringTie\ttranscript\t3052907\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";\n-chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";\n-chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";\n-chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";\n-chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";\n-chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";\n-chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";\n-chr19\tStringTie\texon\t3062172\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";\n-chr19\tStringTie\ttranscript\t3052907\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";\n-chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";\n-chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";\n-chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";\n-chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";\n-chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";\n-chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";\n-chr19\tStringTie\texon\t3062698\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";\n-chr19\tStringTie\ttranscript\t2997664\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";\n-chr19\tStringTie\texon\t2997664\t2997953\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";\n-chr19\tStringTie\texon\t3000645\t3000721\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";\n-chr19\tStringTie\texon\t3002351\t3002501\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";\n-chr19\tStringTie\texon\t3005435\t3005582\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";\n-chr19\tStringTie\texon\t3005719\t3005966\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";\n-chr19\tStringTie\texon\t3006418\t3006667\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";\n-chr19\tStringTie\texon\t3008867\t3008943\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";\n-chr19\tStringTie\texon\t3009540\t3009700\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";\n-chr19\tStringTie\texon\t3011020\t3011158\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";\n-chr19\tStringTie\texon\t3013667\t3013816\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";\n-chr19\tStringTie\texon\t3014568\t3014612\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";\n-chr19\tStringTie\texon\t3015651\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";\n-chr19\tStringTie\ttranscript\t3018960\t3029141\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";\n-chr19\tStringTie\texon\t3018960\t3019461\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";\n-chr19\tStringTie\texon\t3019697\t3019771\t100'..b'3938.679688";\n-chr19\tStringTie\texon\t3366538\t3366664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";\n-chr19\tStringTie\texon\t3381710\t3382241\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";\n-chr19\tStringTie\texon\t3425104\t3425175\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";\n-chr19\tStringTie\texon\t3433516\t3433590\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";\n-chr19\tStringTie\texon\t3434275\t3434398\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";\n-chr19\tStringTie\texon\t3435081\t3435205\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";\n-chr19\tStringTie\texon\t3449012\t3449137\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";\n-chr19\tStringTie\texon\t3452480\t3452664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";\n-chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";\n-chr19\tStringTie\ttranscript\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";\n-chr19\tStringTie\texon\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";\n-chr19\tStringTie\ttranscript\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";\n-chr19\tStringTie\texon\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";\n-chr19\tStringTie\ttranscript\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";\n-chr19\tStringTie\texon\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";\n-chr19\tStringTie\ttranscript\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";\n-chr19\tStringTie\texon\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";\n-chr19\tStringTie\ttranscript\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";\n-chr19\tStringTie\texon\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";\n-chr19\tStringTie\ttranscript\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";\n-chr19\tStringTie\texon\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";\n-chr19\tStringTie\ttranscript\t3490820\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";\n-chr19\tStringTie\texon\t3490820\t3491809\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";\n-chr19\tStringTie\texon\t3492260\t3492497\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";\n-chr19\tStringTie\texon\t3494026\t3494102\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";\n-chr19\tStringTie\texon\t3496539\t3496884\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";\n-chr19\tStringTie\texon\t3500559\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";\n+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";\n+test_chromosome\tStringTie\texon\t53\t250\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";\n+test_chromosome\tStringTie\texon\t351\t400\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";\n+test_chromosome\tStringTie\texon\t501\t550\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";\n' |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Thu Jul 03 18:38:02 2014 -0400 +++ b/test-data/stringtie_out2.gtf Thu Mar 05 11:41:12 2015 -0500 |
| b |
| b'@@ -1,145 +1,4 @@\n-chr19\tStringTie\ttranscript\t3052907\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";\n-chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";\n-chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";\n-chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";\n-chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";\n-chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";\n-chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";\n-chr19\tStringTie\texon\t3062172\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";\n-chr19\tStringTie\ttranscript\t3052907\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";\n-chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";\n-chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";\n-chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";\n-chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";\n-chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";\n-chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";\n-chr19\tStringTie\texon\t3062698\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";\n-chr19\tStringTie\ttranscript\t2997664\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";\n-chr19\tStringTie\texon\t2997664\t2997953\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";\n-chr19\tStringTie\texon\t3000645\t3000721\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";\n-chr19\tStringTie\texon\t3002351\t3002501\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";\n-chr19\tStringTie\texon\t3005435\t3005582\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";\n-chr19\tStringTie\texon\t3005719\t3005966\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";\n-chr19\tStringTie\texon\t3006418\t3006667\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";\n-chr19\tStringTie\texon\t3008867\t3008943\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";\n-chr19\tStringTie\texon\t3009540\t3009700\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";\n-chr19\tStringTie\texon\t3011020\t3011158\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";\n-chr19\tStringTie\texon\t3013667\t3013816\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";\n-chr19\tStringTie\texon\t3014568\t3014612\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";\n-chr19\tStringTie\texon\t3015651\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";\n-chr19\tStringTie\ttranscript\t3018960\t3029141\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";\n-chr19\tStringTie\texon\t3018960\t3019461\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";\n-chr19\tStringTie\texon\t3019697\t3019771\t100'..b'3938.679688";\n-chr19\tStringTie\texon\t3366538\t3366664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";\n-chr19\tStringTie\texon\t3381710\t3382241\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";\n-chr19\tStringTie\texon\t3425104\t3425175\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";\n-chr19\tStringTie\texon\t3433516\t3433590\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";\n-chr19\tStringTie\texon\t3434275\t3434398\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";\n-chr19\tStringTie\texon\t3435081\t3435205\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";\n-chr19\tStringTie\texon\t3449012\t3449137\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";\n-chr19\tStringTie\texon\t3452480\t3452664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";\n-chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";\n-chr19\tStringTie\ttranscript\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";\n-chr19\tStringTie\texon\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";\n-chr19\tStringTie\ttranscript\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";\n-chr19\tStringTie\texon\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";\n-chr19\tStringTie\ttranscript\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";\n-chr19\tStringTie\texon\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";\n-chr19\tStringTie\ttranscript\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";\n-chr19\tStringTie\texon\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";\n-chr19\tStringTie\ttranscript\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";\n-chr19\tStringTie\texon\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";\n-chr19\tStringTie\ttranscript\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";\n-chr19\tStringTie\texon\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";\n-chr19\tStringTie\ttranscript\t3490820\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";\n-chr19\tStringTie\texon\t3490820\t3491809\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";\n-chr19\tStringTie\texon\t3492260\t3492497\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";\n-chr19\tStringTie\texon\t3494026\t3494102\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";\n-chr19\tStringTie\texon\t3496539\t3496884\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";\n-chr19\tStringTie\texon\t3500559\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";\n+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";\n+test_chromosome\tStringTie\texon\t53\t250\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";\n+test_chromosome\tStringTie\texon\t351\t400\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";\n+test_chromosome\tStringTie\texon\t501\t550\t1000\t+\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";\n' |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out3.gtf Thu Mar 05 11:41:12 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; +test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000"; |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out4.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out4.gtf Thu Mar 05 11:41:12 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; +test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000"; |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out5.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out5.gtf Thu Mar 05 11:41:12 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; +test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000"; |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out_coverage.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out_coverage.gtf Thu Mar 05 11:41:12 2015 -0500 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r 62d212192002 -r 9f80c71f1779 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 03 18:38:02 2014 -0400 +++ b/tool_dependencies.xml Thu Mar 05 11:41:12 2015 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="stringtie" version="0.97"> - <repository changeset_revision="bbcdfb50d3f0" name="package_stringtie_0_97" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="stringtie" version="1.0.1"> + <repository changeset_revision="cd94bd10219b" name="package_stringtie_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |