# HG changeset patch
# User bebatut
# Date 1461226873 14400
# Node ID 2a8acb4c0afcd60ce9b80ea05de4eb2bb0236a94
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
diff -r 000000000000 -r 2a8acb4c0afc compute_wilcoxon_test.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_wilcoxon_test.R Thu Apr 21 04:21:13 2016 -0400
@@ -0,0 +1,55 @@
+library('getopt')
+
+option_specification = matrix(c(
+ 'input_file', 'a', 2, 'character',
+ 'output_file', 'b', 2, 'character',
+ 'column1_id', 'c', 2, 'integer',
+ 'column2_id', 'd', 2, 'integer',
+ 'alternative','e',2,'character',
+ 'paired','f',2,'logical',
+ 'exact','g',2,'logical',
+ 'correct','h',2, 'logical',
+ 'mu','i',2,'integer',
+ 'header','y',2,'logical'
+), byrow=TRUE, ncol=4);
+
+options = getopt(option_specification);
+
+header = TRUE
+if(!is.null(options$header)) header = options$header
+
+data = read.table(options$input_file, sep = '\t', h = header)
+
+column1_id = 1
+if(!is.null(options$column1_id)) column1_id = options$column1_id
+x = data[,column1_id]
+y = NULL
+if(!is.null(options$column2_id)) y = data[,options$column2_id]
+
+alternative = 'two.sided'
+if(!is.null(options$alternative)) alternative = options$alternative
+
+mu = 0
+if(!is.null(options$mu)) mu = options$mu
+
+paired = FALSE
+if(!is.null(options$paired)) paired = options$paired
+
+exact = NULL
+if(!is.null(options$exact)) exact = options$exact
+
+correct = TRUE
+if(!is.null(options$correct)) correct = options$correct
+
+test = wilcox.test(x = x, y = y, alternative = alternative, mu = mu,
+ paired = paired, exact = exact, correct = correct)
+
+m = matrix(ncol = 2, nrow = 6)
+m[1,] = c('statistic',test$statistic)
+m[2,] = c('parameter',test$parameter)
+m[3,] = c('p.value',test$p.value)
+m[4,] = c('null.value',test$null.value)
+m[5,] = c('alternative',test$alternative)
+m[6,] = c('method',test$method)
+write.table(m, file = options$output_file, sep = "\t", quote = FALSE,
+ row.names = FALSE, col.names = FALSE)
diff -r 000000000000 -r 2a8acb4c0afc compute_wilcoxon_test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_wilcoxon_test.xml Thu Apr 21 04:21:13 2016 -0400
@@ -0,0 +1,94 @@
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+ with R
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+ R
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diff -r 000000000000 -r 2a8acb4c0afc test-data/input_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_file.txt Thu Apr 21 04:21:13 2016 -0400
@@ -0,0 +1,45 @@
+GO:0000160 phosphorelay signal transduction system 2.24188560912 0.728693934232 2.27727933683 0.749521959908
+GO:0000746 conjugation 0.0994837099605 0.041803266954 0.0153440543392 0.0123485894543
+GO:0000902 cell morphogenesis 8.11126977702e-06 0.0501066555955 4.12343924065e-05 0.0426587635694
+GO:0002376 immune system process 0.085489980287 0.0 0.0275218309404 0.00149679872174
+GO:0005975 carbohydrate metabolic process 3.93695964707 3.53466664758 3.82956086917 4.33023870198
+GO:0006091 generation of precursor metabolites and energy 1.07156623777 1.0906071495 1.17950701314 1.06085609403
+GO:0006259 DNA metabolic process 7.83088558928 5.06907560378 7.58396051319 4.27934754543
+GO:0006412 translation 4.20183364466 2.74183619419 5.03906963774 3.04486279969
+GO:0006520 cellular amino acid metabolic process 6.18101744575 3.82270833632 6.27139841544 3.78690076599
+GO:0006629 lipid metabolic process 2.22295409952 0.98294942091 2.54389716799 1.18920658442
+GO:0006790 sulfur compound metabolic process 1.45678041362 0.428626648151 1.37494525671 0.342766907277
+GO:0006807 nitrogen compound metabolic process 6.29928644413 17.1144292852 6.08311422603 15.9266867986
+GO:0006810 transport 4.61323317367 8.81648079483 3.18084754012 8.87713901893
+GO:0006811 ion transport 2.84530948465 1.81185666634 2.90259750702 1.89008258587
+GO:0006935 chemotaxis 0.00293746066557 0.132567894519 0.0120376618448 0.0841949280975
+GO:0006950 response to stress 1.94565920911 1.44736653735 2.0733055949 1.4305653783
+GO:0007154 cell communication 0.721015903582 1.15674793488 0.709743568009 1.18696138634
+GO:0007165 signal transduction 0.118779041384 1.12181643785 0.0745544227737 1.16488360519
+GO:0009056 catabolic process 2.8187943392 1.45624257348 2.98058889328 1.56752246133
+GO:0009058 biosynthetic process 19.0004196424 14.2414568152 19.1704185155 13.7907550227
+GO:0009117 nucleotide metabolic process 3.44391451912 1.42846917009 3.70529753166 1.38640981601
+GO:0009306 protein secretion 0.0636027918464 0.176375427696 0.0756710986973 0.150802471215
+GO:0009404 toxin metabolic process 0.03091092162 0.014316187313 0.0362106070805 0.0130969888151
+GO:0009405 pathogenesis 1.43460861083 0.541438204177 0.368367078771 0.122737495182
+GO:0015979 photosynthesis 0.232009822868 0.0798843252065 0.167653248687 0.0703495399215
+GO:0016032 viral process 0.00123963164065 0.0128845685817 0.00242960292976 0.0134711884956
+GO:0016043 cellular component organization 2.24641451781 0.697770969635 2.38025522473 0.654101041398
+GO:0016049 cell growth 0.000155245877721 0.0 0.0420673650671 0.0
+GO:0016070 RNA metabolic process 2.37121554921 5.80206439421 2.38215565603 5.74546189338
+GO:0016310 phosphorylation 2.50223255226 0.848090936421 1.9906050825 0.866646459884
+GO:0019538 protein metabolic process 2.25811799055 5.09713533092 1.9377105334 5.82741162339
+GO:0022900 electron transport chain 0.3062712212 0.360767920287 0.237876158003 0.278030362562
+GO:0030031 cell projection assembly 0.0642099836606 0.0355041445362 0.0413581109156 0.0142195878565
+GO:0032196 transposition 0.722175839172 0.299208314842 2.633467426 0.919782814506
+GO:0042592 homeostatic process 0.991966070514 0.362485862765 0.715433785162 0.325553721977
+GO:0043934 sporulation 0.0768001451434 0.0160341297906 0.0916709924953 0.00673559424781
+GO:0044281 small molecule metabolic process 6.91812462508 7.90797554796 7.74857313252 8.04978352548
+GO:0045333 cellular respiration 0.338287752671 0.686031696039 0.175606167551 0.522008554205
+GO:0046034 ATP metabolic process 1.36885696133 0.377661021316 1.37948961282 0.321811725173
+GO:0048870 cell motility 0.322410195844 0.136003779473 0.153352240024 0.0722205383237
+GO:0051186 cofactor metabolic process 4.61150014233 1.60312665531 4.55766657384 1.41821678885
+GO:0051301 cell division 1.32835952519 0.120828620922 1.26384039624 0.0942983194692
+GO:0055114 oxidation-reduction process 0.131832728405 7.08823066241 0.300772862677 7.94837541209
+GO:0071554 cell wall organization or biogenesis 0.00369855395882 0.456400051538 0.0153325835178 0.403387255508
+GO:0071941 nitrogen cycle metabolic process 0.5367849148 0.0612732816996 0.267403669367 0.0160905862586
diff -r 000000000000 -r 2a8acb4c0afc test-data/two_sided_two_columns_test_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_sided_two_columns_test_output.txt Thu Apr 21 04:21:13 2016 -0400
@@ -0,0 +1,6 @@
+statistic 981
+parameter parameter
+p.value 0.916918193979449
+null.value 0
+alternative two.sided
+method Wilcoxon rank sum test with continuity correction
diff -r 000000000000 -r 2a8acb4c0afc tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Apr 21 04:21:13 2016 -0400
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