Mercurial > repos > artbio > fishertest

annotate fisher_test.xml @ 1:3a67bee2ef63 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 6215dff88ce7276f36f5793d8475d4da2c1c9292"
author artbio
date Mon, 22 Jun 2020 08:48:38 -0400
parents 5f784a95ce13
children 8052d037517f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3a67bee2ef63 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 6215dff88ce7276f36f5793d8475d4da2c1c9292"
artbio
parents: 0
diff changeset
1 <tool id="fishertest" name="Fisher's exact test" version="1.1.0">
0
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
2 <description>on two gene hit lists</description>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
3 <requirements>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
4 <!-- <requirement type="package" version="3.1.2">R</requirement> -->
1
3a67bee2ef63 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 6215dff88ce7276f36f5793d8475d4da2c1c9292"
artbio
parents: 0
diff changeset
5 <requirement type="package" version="2.18.0=r36_1">bioconductor-qvalue</requirement>
0
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
6 </requirements>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
7 <command><![CDATA[
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
8 Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}"
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
9 ]]></command>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
10 <configfiles>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
11 <configfile name="fisher_test">
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
12 <![CDATA[
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
13 ## Setup R error handling to go to stderr
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
14 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
15 options(warn=-1)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
16 suppressMessages(library(qvalue))
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
17 library(parallel)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
18 args = commandArgs(trailingOnly = TRUE)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
19 slots = as.numeric(args[1])
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
20 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE, stringsAsFactor = TRUE)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
21 depth1 = sum(countsTable[,2])
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
22 depth2 = sum(countsTable[,3])
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
23 float_table=data.frame(countsTable[,2], countsTable[,3])
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
24
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
25 calc_pvalue <- function(row, depth1, depth2, ... ){
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
26 thearray = array( c(row, (depth1 - row[1]), (depth2 - row[2])), dim=c(2,2))
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
27 current_test = fisher.test( thearray )
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
28 return(current_test\$p.value)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
29 }
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
30
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
31 cl <- makePSOCKcluster(slots)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
32 clusterExport(cl=cl, varlist=c("calc_pvalue", "depth1", "depth2"))
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
33 ptm <- proc.time()
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
34 p_val = parApply(cl, float_table, 1, function(x) calc_pvalue(x, depth1, depth2))
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
35 stopCluster(cl)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
36 proc.time() - ptm
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
37 p_val[p_val>1]=1
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
38 p = qvalue(p_val)
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
39 finalTable = cbind(countsTable, data.frame(p\$pvalues), data.frame(p\$qvalues))
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
40 write.table ( finalTable, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
41 ]]>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
42 </configfile>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
43 </configfiles>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
44 <inputs>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
45 <param name="input" type="data" format="tabular" label="gene hit lists, 2 samples"/>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
46 </inputs>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
47 <outputs>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
48 <data name="output" format="tabular" label="Fisher test p-values" />
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
49 </outputs>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
50 <tests>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
51 <test>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
52 <param name="input" value="counts.tab" ftype="tabular"/>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
53 <output name="output" file="fisher.tab" ftype="tabular"/>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
54 </test>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
55 </tests>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
56 <help>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
57
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
58 **What it does**
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
59
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
60 Runs Fisher's exact test for testing the null of independence of rows and columns in a contingency table of two columns.
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
61
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
62 p.pvalues: the chance of getting this data if it is independent between columns (false negative); the p-value.
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
63
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
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.
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
65
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
66 Be aware that this test does not take into account the biological noise that would be visible if replicates were available.
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
67
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
68
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
69 </help>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
70 <citations>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
71 <citation type="doi">10.1111/1467-9868.00346</citation>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
72 </citations>
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
73
5f784a95ce13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
artbio
parents:
diff changeset
74 </tool>