Mercurial > repos > iuc > trinity_analyze_diff_expr
changeset 11:284bb0c05da9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
| author | iuc |
|---|---|
| date | Fri, 01 Nov 2019 08:12:28 -0400 |
| parents | dc0f01791c9b |
| children | de949e8c076d |
| files | analyze_diff_expr.xml macros.xml test-data/count/contig_exn50_statistic/ExN50.stats test-data/supertranscripts/trinity_genes.fasta test-data/supertranscripts/trinity_genes.gtf |
| diffstat | 5 files changed, 18 insertions(+), 17 deletions(-) [+] |
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--- a/analyze_diff_expr.xml Fri Apr 26 06:45:46 2019 -0400 +++ b/analyze_diff_expr.xml Fri Nov 01 08:12:28 2019 -0400 @@ -4,10 +4,10 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement> - <requirement type="package" version="1.30.0">bioconductor-goseq</requirement> - <requirement type="package" version="2.0.6">r-cluster</requirement> - <requirement type="package" version="1.1.24">r-fastcluster</requirement> + <requirement type="package" version="2.16.0">bioconductor-qvalue</requirement> + <requirement type="package" version="1.36.0">bioconductor-goseq</requirement> + <requirement type="package" version="2.0.8">r-cluster</requirement> + <requirement type="package" version="1.1.25">r-fastcluster</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ ## DE results input files must be in the working directory and have suffix .DE_results
--- a/macros.xml Fri Apr 26 06:45:46 2019 -0400 +++ b/macros.xml Fri Nov 01 08:12:28 2019 -0400 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.8.4</token> + <token name="@WRAPPER_VERSION@">2.8.5</token> <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> #if $pool.inputs.strand.is_strand_specific:
--- a/test-data/count/contig_exn50_statistic/ExN50.stats Fri Apr 26 06:45:46 2019 -0400 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Fri Nov 01 08:12:28 2019 -0400 @@ -1,4 +1,5 @@ Ex ExN50 num_transcripts 33 541 1 67 541 2 +99 380 3 100 279 7
--- a/test-data/supertranscripts/trinity_genes.fasta Fri Apr 26 06:45:46 2019 -0400 +++ b/test-data/supertranscripts/trinity_genes.fasta Fri Nov 01 08:12:28 2019 -0400 @@ -1,14 +1,14 @@ ->TRINITY_DN1_c0_g1 -CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN2_c3_g1 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA >TRINITY_DN0_c0_g1 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC >TRINITY_DN2_c0_g1 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ->TRINITY_DN2_c1_g1 -GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN3_c0_g1 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT >TRINITY_DN2_c2_g1 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC ->TRINITY_DN2_c3_g1 -GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1 -ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +>TRINITY_DN2_c1_g1 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN1_c0_g1 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
--- a/test-data/supertranscripts/trinity_genes.gtf Fri Apr 26 06:45:46 2019 -0400 +++ b/test-data/supertranscripts/trinity_genes.gtf Fri Nov 01 08:12:28 2019 -0400 @@ -1,14 +1,14 @@ -TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" +TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" TRINITY_DN0_c0_g1 Trinity_gene exon 1 229 . + . gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1" TRINITY_DN2_c0_g1 Trinity_gene exon 1 279 . + . gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1" -TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" +TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" TRINITY_DN2_c2_g1 Trinity_gene exon 1 240 . + . gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1" -TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" +TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" -TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" +TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"