Mercurial > repos > drosofff > fishertest
changeset 0:8cb991523c5a draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit f9c229fc39114e80cf01383d7240e4971b2e3c53
| author | drosofff |
|---|---|
| date | Thu, 09 Mar 2017 12:31:03 -0500 |
| parents | |
| children | |
| files | fisher_test.xml test-data/counts.tab test-data/fisher.tab tool_dependencies.xml |
| diffstat | 4 files changed, 1084 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fisher_test.xml Thu Mar 09 12:31:03 2017 -0500 @@ -0,0 +1,75 @@ +<tool id="fishertest" name="Fisher's exact test" version="0.9.0"> + <description>on two gene hit lists</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2.14">biocbasics</requirement> + <requirement type="package" version="2.4.2=r3.3.1_0">bioconductor-qvalue</requirement> + </requirements> + <command><![CDATA[ + Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}" + ]]></command> + <configfiles> + <configfile name="fisher_test"> + <![CDATA[ + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + options(warn=-1) + suppressMessages(library(qvalue)) + library(parallel) + args = commandArgs(trailingOnly = TRUE) + slots = as.numeric(args[1]) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE, stringsAsFactor = TRUE) + depth1 = sum(countsTable[,2]) + depth2 = sum(countsTable[,3]) + float_table=data.frame(countsTable[,2], countsTable[,3]) + + calc_pvalue <- function(row, depth1, depth2, ... ){ + thearray = array( c(row, (depth1 - row[1]), (depth2 - row[2])), dim=c(2,2)) + current_test = fisher.test( thearray ) + return(current_test\$p.value) + } + + cl <- makePSOCKcluster(slots) + clusterExport(cl=cl, varlist=c("calc_pvalue", "depth1", "depth2")) + ptm <- proc.time() + p_val = parApply(cl, float_table, 1, function(x) calc_pvalue(x, depth1, depth2)) + stopCluster(cl) + proc.time() - ptm + p_val[p_val>1]=1 + p = qvalue(p_val) + finalTable = cbind(countsTable, data.frame(p\$pvalues), data.frame(p\$qvalues)) + write.table ( finalTable, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + ]]> + </configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="gene hit lists, 2 samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="Fisher test p-values" /> + </outputs> +<tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <output name="output" file="fisher.tab" ftype="tabular"/> + </test> +</tests> +<help> + +**What it does** + +Runs Fisher's exact test for testing the null of independence of rows and columns in a contingency table of two columns. + +p.pvalues: the chance of getting this data if it is independent between columns (false negative); the p-value. + +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. + +Be aware that this test does not take into account the biological noise that would be visible if replicates were available. + + +</help> +<citations> + <citation type="doi">10.1111/1467-9868.00346</citation> +</citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Thu Mar 09 12:31:03 2017 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 4: Pronuclei 1: accepted_hits +NM_001195025 0 0 +NM_028778 0 0 +NM_001290393 0 0 +NM_008922 3133 2288 +NM_175370 4 7 +NM_001290390 0 0 +NM_175642 977 1013 +NM_001290392 0 0 +NM_027671 0 0 +NM_178884 0 0 +NM_199021 332 1436 +NM_198680 0 0 +NM_011465 0 0 +NM_130890 0 0 +NM_001113393 0 0 +NM_001113392 0 0 +NM_001113391 19 88 +NM_031162 0 0 +NR_103716 0 0 +NM_001160371 0 0 +NM_177834 1 2 +NM_145381 606 367 +NM_177173 0 0 +NM_001160369 0 0 +NM_001160370 2 9 +NM_001289497 0 0 +NM_027974 0 6 +NM_133235 74 0 +NM_028096 77 2 +NM_201365 1 0 +NM_001126046 0 0 +NM_001081198 31 144 +NM_001160386 890 1226 +NM_009418 456 774 +NM_001114663 369 353 +NM_001252070 346 463 +NR_045151 0 0 +NM_001081050 93 35 +NM_007642 0 0 +NM_025728 0 0 +NM_029160 0 0 +NM_175210 290 346 +NM_010154 31 23 +NM_175291 0 0 +NM_010472 265 1666 +NM_023314 0 20 +NM_027456 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Mar 09 12:31:03 2017 -0500 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="biocbasics" version="2.14"> + <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>