Mercurial > repos > bebatut > compute_wilcoxon_test
changeset 0:2a8acb4c0afc draft default tip
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
| author | bebatut |
|---|---|
| date | Thu, 21 Apr 2016 04:21:13 -0400 |
| parents | |
| children | |
| files | compute_wilcoxon_test.R compute_wilcoxon_test.xml test-data/input_file.txt test-data/two_sided_two_columns_test_output.txt tool_dependencies.xml |
| diffstat | 5 files changed, 209 insertions(+), 0 deletions(-) [+] |
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--- /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)
--- /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 @@ +<tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0"> + <description>with R</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + + <version_command></version_command> + + <command><![CDATA[ + Rscript $__tool_directory__/compute_wilcoxon_test.R + --input_file $input_file + --header $header + --output_file $output_file + --column1_id $column1_id + + #if $add_column.add_column_test == "true": + --column2_id $add_column.column2_id + --paired $add_column.paired + #end if + + --alternative "$alternative" + --mu $mu + + --exact $exact + --correct $correct + + ]]></command> + + <inputs> + <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/> + + <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/> + + <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/> + + <conditional name="add_column"> + <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/> + <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/> + </when> + <when value="false" /> + </conditional> + + <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)"> + <option value="two.sided" selected="true">Two sided</option> + <option value="greater">Greater</option> + <option value="less">Less</option> + </param> + <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/> + + <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/> + <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/> + </inputs> + + <outputs> + <data name="output_file" format="txt" label="${tool.name} on ${on_string}: Wilcox test result" /> + </outputs> + + <tests> + <test> + <param name="input_file" ftype="tabular" value="input_file.txt"/> + <param name="header" value="TRUE"/> + <param name="column1_id" value="3"/> + <param name="add_column_test" value="true"/> + <param name="column2_id" value="5"/> + <param name="paired" value="FALSE"/> + <param name="alternative" value="two.sided"/> + <param name="mu" value="0"/> + <param name="exact" value="FALSE"/> + <param name="correct" value="TRUE"/> + <output name="output_file" file="two_sided_two_columns_test_output.txt"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +This tool compute a Wilcoxon test with R's wilcox.test function. + ]]></help> + + <citations> + </citations> +</tool>
--- /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
--- /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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Apr 21 04:21:13 2016 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.1"> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="r-getopt" version="1.20.0"> + <repository changeset_revision="712cb82311a8" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>