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author artbio
date Sat, 14 Oct 2023 18:00:34 +0000
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8faa01102fbc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization commit 770f615298b9314baec54a539adcb2c3d0e729a7
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1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.40.2+galaxy0" profile="22.01">
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2 <description>of hit lists (geometric method)</description>
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3 <requirements>
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4 <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command>
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10 <configfiles>
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11 <configfile name="normalizationDESeq">
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12 ## Setup R error handling to go to stderr
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13 options(show.error.messages =FALSE, error = function(){
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14 cat(geterrmessage(), file=stderr())
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15 q("no", 1, FALSE)
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16 }
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17 )
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18 suppressMessages(require(DESeq2))
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19 countsTable = read.delim("${input}", header = TRUE, check.names = FALSE)
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20 rownames(countsTable ) = countsTable[,1]
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21 countsTable = countsTable[, -1]
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22 conds = factor(c(rep("C", length(countsTable[1, ]) - 1), "T"))
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23 cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds)
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24 cds = estimateSizeFactors( cds )
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25 write.table(as.data.frame(sizeFactors(cds)), file = "${output_factors}", row.names = TRUE,
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26 col.names = TRUE, quote = FALSE, dec = ".", sep = "\t", eol = "\n")
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27 norm_table = as.data.frame(counts( cds, normalized=TRUE ))
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28 norm_table = cbind(rownames(norm_table), norm_table)
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29 colnames(norm_table) = c("gene", colnames(countsTable))
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30 write.table(norm_table, file = "${norm_hit_table}", row.names = FALSE, col.names = TRUE,
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31 quote = FALSE, dec = ".", sep = "\t", eol = "\n")
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32 </configfile>
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33 </configfiles>
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34 <inputs>
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35 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
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36 </inputs>
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37 <outputs>
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38 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
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39 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input" value="counts.tab" ftype="tabular"/>
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44 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
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45 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
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46 </test>
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47 </tests>
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48 <help>
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50 **What it does**
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52 DESeq2_normalization takes a tabular table of raw read counts (integers), each column corresponding to a sample count,
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53 and returns (1) the DESeq2 Size Factors (geometic mean method) and (2) a normalized table (floatting number)
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54 of counts.
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56 **Inputs**
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58 The following table gives an example of the tabular input that has to be provided to the tool:
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60 <![CDATA[
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62 Geneid Oocyte 1 Oocyte 2 Pronuclei 1 pronuclei 2
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64 NM_001195025 0 0 0 0
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66 NM_028778 0 0 0 0
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68 NM_001290393 0 0 0 0
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70 NM_008922 3133 2276 2288 2659
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72 NM_175370 4 22 7 16
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74 NM_001290390 0 0 0 0
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76 NM_175642 977 1711 1013 459
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78 NM_001290392 0 0 0 0
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80 NM_027671 0 0 0 0
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82 NM_178884 0 0 0 2
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84 NM_199021 332 413 1436 836
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86 NM_198680 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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87
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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88 NM_011465 0 4 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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89
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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90 NM_130890 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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91
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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92 NM_001113393 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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93
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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94 NM_001113392 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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95
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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96 NM_001113391 19 3 88 15
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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97
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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98 NM_031162 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
diff changeset
99
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
diff changeset
100 NR_103716 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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101
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
diff changeset
102 NM_001160371 0 0 0 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
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103
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
diff changeset
104 NM_177834 1 3 2 0
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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105
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
diff changeset
106 NM_145381 606 445 367 306
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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107
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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108 ]]>
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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109
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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110
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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111 </help>
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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112 <citations>
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
parents:
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113 <citation type="doi">10.1186/s13059-014-0550-8</citation>
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
artbio
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114 </citations>
6b990f6c6ba9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
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115 </tool>