| Previous changeset 3:83fa9ede1259 (2016-12-13) Next changeset 5:2be382e6918a (2017-03-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0 |
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modified:
run_de_analysis.xml |
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added:
test-data/count/contig_exn50_statistic/ExN50.stats test-data/count/contig_exn50_statistic/Trinity.fasta test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix |
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| diff -r 83fa9ede1259 -r 36b2700b604d run_de_analysis.xml --- a/run_de_analysis.xml Tue Dec 13 14:43:56 2016 -0500 +++ b/run_de_analysis.xml Thu Mar 23 10:16:19 2017 -0400 |
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| @@ -5,7 +5,6 @@ </macros> <expand macro="requirements"> <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> - <requirement type="package" version="1.10.0">deseq2</requirement> <requirement type="package" version="3.14.0">bioconductor-edger</requirement> <requirement type="package" version="3.28.10">bioconductor-limma</requirement> <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> |
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| diff -r 83fa9ede1259 -r 36b2700b604d test-data/count/contig_exn50_statistic/ExN50.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Thu Mar 23 10:16:19 2017 -0400 |
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| @@ -0,0 +1,5 @@ +#E min_expr E-N50 num_transcripts +E33 525311.050 541 1 +E67 525311.050 541 2 +E99 329523.810 380 3 +E100 0 279 7 |
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| diff -r 83fa9ede1259 -r 36b2700b604d test-data/count/contig_exn50_statistic/Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/Trinity.fasta Thu Mar 23 10:16:19 2017 -0400 |
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| @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT + |
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| diff -r 83fa9ede1259 -r 36b2700b604d test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix Thu Mar 23 10:16:19 2017 -0400 |
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| @@ -0,0 +1,8 @@ + sample_A sample_B +TRINITY_DN2_c2_g1_i1 525311.050 145165.140 +TRINITY_DN2_c1_g1_i1 145165.140 525311.050 +TRINITY_DN2_c0_g1_i1 0.000 0.000 +TRINITY_DN1_c0_g1_i1 329523.810 329523.810 +TRINITY_DN3_c0_g1_i1 0.000 0.000 +TRINITY_DN2_c3_g1_i1 0.000 0.000 +TRINITY_DN0_c0_g1_i1 0.000 0.000 |