Mercurial > repos > mvdbeek > deseq_with_replicates

annotate replicateDESeq.xml @ 0:da2dbe13adc2 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Sat, 05 Mar 2016 07:02:52 -0500
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da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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1 <tool id="replicateDESeq" name="DESeq1 Profiling (replicates)" version="1.0.1">
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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2 <description>with sample replicates</description>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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3 <requirements>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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4 <requirement type="package" version="3.1.2">R</requirement>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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5 <requirement type="package" version="2.14">biocbasics</requirement>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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6 </requirements>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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7 <command>Rscript $replicateDESeq </command>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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8 <inputs>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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9 <param name="input" type="data" format="tabular" label="gene readcount list, more than 2 samples"/>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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10 <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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11 </inputs>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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12 <outputs>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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13 <data name="output" format="tabular" label="DESeq differential calling" />
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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14 </outputs>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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15 <tests>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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16 <test>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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17 <param name="input" value="counts.tab" ftype="tabular"/>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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18 <param name="expPlan" value="CCTTT"/>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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19 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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20 </test>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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21 </tests>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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22 <configfiles>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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23 <configfile name="replicateDESeq">
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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24 ## Setup R error handling to go to stderr
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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25 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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26 suppressMessages(require(DESeq))
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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27 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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28 rownames( countsTable )= countsTable[,1]
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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29 countsTable= countsTable[ , -1 ]
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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30 stringconds = "${expPlan}"
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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31 conds = unlist(strsplit(stringconds, split=""))
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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32 cds = newCountDataSet( countsTable, conds )
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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33 cds = estimateSizeFactors( cds )
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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34 cds = estimateDispersions( cds, method="per-condition", sharingMode="maximum") ## was fit-only before 9-12-2013 !! tried for RNAseq - Actually does not change anything !
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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35 ## Attention: fitType="local" is added when parametricDispersionFit fails. remove after use !
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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36 res = nbinomTest( cds, "C", "T" )
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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37 # resNA = res[-which(is.na(res[,8])),] ## omitted the NA lignes, but this was causing a full delete of the table completely devoid of NA !! (not logical but true)
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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38 write.table ( res[order(res[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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39 </configfile>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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40 </configfiles>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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41 <help>
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42
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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43 **What it does**
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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44
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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45 DESeq differential calling (order by padj, ascending), on more than two samples, with replicates.
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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46
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47
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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48 </help>
da2dbe13adc2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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49 </tool>