Mercurial > repos > iuc > trinity_run_de_analysis

changeset 4:36b2700b604d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
author iuc
date Thu, 23 Mar 2017 10:16:19 -0400
parents 83fa9ede1259
children 2be382e6918a
files run_de_analysis.xml 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
diffstat 4 files changed, 59 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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>
--- /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
@@ -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
--- /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
@@ -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
+
--- /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
@@ -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