Mercurial > repos > artbio > fishertest
comparison fisher_test.xml @ 0:5f784a95ce13 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
author | artbio |
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date | Mon, 28 Aug 2017 13:25:56 -0400 |
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children | 3a67bee2ef63 |
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1 <tool id="fishertest" name="Fisher's exact test" version="1.0.0"> | |
2 <description>on two gene hit lists</description> | |
3 <requirements> | |
4 <!-- <requirement type="package" version="3.1.2">R</requirement> --> | |
5 <requirement type="package" version="2.4.2=r3.3.1_0">bioconductor-qvalue</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}" | |
9 ]]></command> | |
10 <configfiles> | |
11 <configfile name="fisher_test"> | |
12 <![CDATA[ | |
13 ## Setup R error handling to go to stderr | |
14 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
15 options(warn=-1) | |
16 suppressMessages(library(qvalue)) | |
17 library(parallel) | |
18 args = commandArgs(trailingOnly = TRUE) | |
19 slots = as.numeric(args[1]) | |
20 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE, stringsAsFactor = TRUE) | |
21 depth1 = sum(countsTable[,2]) | |
22 depth2 = sum(countsTable[,3]) | |
23 float_table=data.frame(countsTable[,2], countsTable[,3]) | |
24 | |
25 calc_pvalue <- function(row, depth1, depth2, ... ){ | |
26 thearray = array( c(row, (depth1 - row[1]), (depth2 - row[2])), dim=c(2,2)) | |
27 current_test = fisher.test( thearray ) | |
28 return(current_test\$p.value) | |
29 } | |
30 | |
31 cl <- makePSOCKcluster(slots) | |
32 clusterExport(cl=cl, varlist=c("calc_pvalue", "depth1", "depth2")) | |
33 ptm <- proc.time() | |
34 p_val = parApply(cl, float_table, 1, function(x) calc_pvalue(x, depth1, depth2)) | |
35 stopCluster(cl) | |
36 proc.time() - ptm | |
37 p_val[p_val>1]=1 | |
38 p = qvalue(p_val) | |
39 finalTable = cbind(countsTable, data.frame(p\$pvalues), data.frame(p\$qvalues)) | |
40 write.table ( finalTable, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") | |
41 ]]> | |
42 </configfile> | |
43 </configfiles> | |
44 <inputs> | |
45 <param name="input" type="data" format="tabular" label="gene hit lists, 2 samples"/> | |
46 </inputs> | |
47 <outputs> | |
48 <data name="output" format="tabular" label="Fisher test p-values" /> | |
49 </outputs> | |
50 <tests> | |
51 <test> | |
52 <param name="input" value="counts.tab" ftype="tabular"/> | |
53 <output name="output" file="fisher.tab" ftype="tabular"/> | |
54 </test> | |
55 </tests> | |
56 <help> | |
57 | |
58 **What it does** | |
59 | |
60 Runs Fisher's exact test for testing the null of independence of rows and columns in a contingency table of two columns. | |
61 | |
62 p.pvalues: the chance of getting this data if it is independent between columns (false negative); the p-value. | |
63 | |
64 q.qvalues: FDR (Faslse Detection Rate) adjusted p-values; a q-value of 0.05 implies that 5% of significant tests will result in false positives. | |
65 | |
66 Be aware that this test does not take into account the biological noise that would be visible if replicates were available. | |
67 | |
68 | |
69 </help> | |
70 <citations> | |
71 <citation type="doi">10.1111/1467-9868.00346</citation> | |
72 </citations> | |
73 | |
74 </tool> |