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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
author artbio
date Mon, 08 Jan 2018 04:21:24 -0500
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1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.0.0">
2 <description>of hit lists (geometric method)</description>
3 <requirements>
4 <requirement type="package" version="1.8.2gx=r3.2.1_0">bioconductor-deseq2</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command>
10 <configfiles>
11 <configfile name="normalizationDESeq">
12 ## Setup R error handling to go to stderr
13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
14 suppressMessages(require(DESeq2))
15 countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
16 rownames( countsTable )= countsTable[,1]
17 countsTable= countsTable[ , -1 ]
18 conds = factor(c(rep ("C", length(countsTable[1,])-1 ), "T"))
19 cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds)
20 cds = estimateSizeFactors( cds )
21 write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
22 norm_table = as.data.frame(counts( cds, normalized=TRUE ))
23 norm_table = cbind(rownames(norm_table), norm_table)
24 colnames(norm_table) = c("gene", colnames(countsTable) )
25 write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
26 </configfile>
27 </configfiles>
28 <inputs>
29 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
30 </inputs>
31 <outputs>
32 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
33 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
34 </outputs>
35 <tests>
36 <test>
37 <param name="input" value="counts.tab" ftype="tabular"/>
38 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
39 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
40 </test>
41 </tests>
42 <help>
43
44 **What it does**
45
46 DESeq2_normalization takes a tabular table of raw read counts (integers), each column corresponding to a sample count,
47 and returns (1) the DESeq2 Size Factors (geometic mean method) and (2) a normalized table (floatting number)
48 of counts.
49
50 **Inputs**
51
52 The following table gives an example of the tabular input that has to be provided to the tool:
53
54 <![CDATA[
55
56 Geneid Oocyte 1 Oocyte 2 Pronuclei 1 pronuclei 2
57
58 NM_001195025 0 0 0 0
59
60 NM_028778 0 0 0 0
61
62 NM_001290393 0 0 0 0
63
64 NM_008922 3133 2276 2288 2659
65
66 NM_175370 4 22 7 16
67
68 NM_001290390 0 0 0 0
69
70 NM_175642 977 1711 1013 459
71
72 NM_001290392 0 0 0 0
73
74 NM_027671 0 0 0 0
75
76 NM_178884 0 0 0 2
77
78 NM_199021 332 413 1436 836
79
80 NM_198680 0 0 0 0
81
82 NM_011465 0 4 0 0
83
84 NM_130890 0 0 0 0
85
86 NM_001113393 0 0 0 0
87
88 NM_001113392 0 0 0 0
89
90 NM_001113391 19 3 88 15
91
92 NM_031162 0 0 0 0
93
94 NR_103716 0 0 0 0
95
96 NM_001160371 0 0 0 0
97
98 NM_177834 1 3 2 0
99
100 NM_145381 606 445 367 306
101
102 ]]>
103
104
105 </help>
106 <citations>
107 <citation type="doi">10.1186/s13059-014-0550-8</citation>
108 </citations>
109 </tool>