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comparison deseq2_normalization.xml @ 2:8faa01102fbc draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization commit 770f615298b9314baec54a539adcb2c3d0e729a7
author artbio
date Sat, 14 Oct 2023 18:00:34 +0000
parents ca845e480c89
children
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1:ca845e480c89 2:8faa01102fbc
1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.0.1"> 1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.40.2+galaxy0" profile="22.01">
2 <description>of hit lists (geometric method)</description> 2 <description>of hit lists (geometric method)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.8.2gx=r3.2.1_0">bioconductor-deseq2</requirement> 4 <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio> 8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command> 9 <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command>
10 <configfiles> 10 <configfiles>
11 <configfile name="normalizationDESeq"> 11 <configfile name="normalizationDESeq">
12 ## Setup R error handling to go to stderr 12 ## Setup R error handling to go to stderr
13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) 13 options(show.error.messages =FALSE, error = function(){
14 cat(geterrmessage(), file=stderr())
15 q("no", 1, FALSE)
16 }
17 )
14 suppressMessages(require(DESeq2)) 18 suppressMessages(require(DESeq2))
15 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) 19 countsTable = read.delim("${input}", header = TRUE, check.names = FALSE)
16 rownames( countsTable )= countsTable[,1] 20 rownames(countsTable ) = countsTable[,1]
17 countsTable= countsTable[ , -1 ] 21 countsTable = countsTable[, -1]
18 conds = factor(c(rep ("C", length(countsTable[1,])-1 ), "T")) 22 conds = factor(c(rep("C", length(countsTable[1, ]) - 1), "T"))
19 cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds) 23 cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds)
20 cds = estimateSizeFactors( cds ) 24 cds = estimateSizeFactors( cds )
21 write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") 25 write.table(as.data.frame(sizeFactors(cds)), file = "${output_factors}", row.names = TRUE,
26 col.names = TRUE, quote = FALSE, dec = ".", sep = "\t", eol = "\n")
22 norm_table = as.data.frame(counts( cds, normalized=TRUE )) 27 norm_table = as.data.frame(counts( cds, normalized=TRUE ))
23 norm_table = cbind(rownames(norm_table), norm_table) 28 norm_table = cbind(rownames(norm_table), norm_table)
24 colnames(norm_table) = c("gene", colnames(countsTable) ) 29 colnames(norm_table) = c("gene", colnames(countsTable))
25 write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") 30 write.table(norm_table, file = "${norm_hit_table}", row.names = FALSE, col.names = TRUE,
31 quote = FALSE, dec = ".", sep = "\t", eol = "\n")
26 </configfile> 32 </configfile>
27 </configfiles> 33 </configfiles>
28 <inputs> 34 <inputs>
29 <param name="input" type="data" format="tabular" label="Hit lists of items"/> 35 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
30 </inputs> 36 </inputs>