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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Sat, 05 Mar 2016 07:00:59 -0500
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d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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1 <tool id="simpleDESeq" name="DESeq Profiling" version="1.0.2" hidden="true">
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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2 <description>2 samples / no replicates</description>
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mvdbeek
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="3.1.2">R</requirement>
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5 <requirement type="package" version="2.14">biocbasics</requirement>
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6 </requirements>
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mvdbeek
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7 <command interpreter="Rscript">$simpleDESeq </command>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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8 <inputs>
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9 <param name="input" type="data" format="tabular" label="readcount lists, 2 samples"/>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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10 </inputs>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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11 <outputs>
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12 <data name="output" format="tabular" label="DESeq differential calling" />
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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13 </outputs>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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14 <tests>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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15 <test>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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16 <param name="input" value="counts.tab" ftype="tabular"/>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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17 <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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18 </test>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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19 </tests>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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20 <configfiles>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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21 <configfile name="simpleDESeq">
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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22 ## Setup R error handling to go to stderr
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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23 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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24 suppressMessages(require(DESeq))
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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25 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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26 rownames( countsTable )= countsTable[,1]
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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27 countsTable= countsTable[ , -1 ]
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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28 conds = c("C","T")
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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29 cds = newCountDataSet( countsTable, conds )
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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30 cds = estimateSizeFactors( cds )
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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31 cds = estimateDispersions( cds, method="blind", sharingMode="fit-only" ) #fitType="local" when dispersion fucks the test. Otherwise DESeq performs a parametric fit using a gamma-family GLM
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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32 res = nbinomTest( cds, "C", "T" )
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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33 resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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34 write.table ( resNA[order(resNA[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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35 </configfile>
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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36 </configfiles>
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37 <help>
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38
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39 **What it does**
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40
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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41 DESeq (version 1) differential calling (order by padj, ascending), on two samples, no replicate
d00e0214e517 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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42 </help>
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43 </tool>