<tool id="DESeq_normalization" name="DESeq Normalization" version="1.0.2">
	<description>of hit lists (geometric method)</description>
        <requirements>
          <requirement type="package" version="3.1.2">R</requirement>
          <requirement type="package" version="2.14">biocbasics</requirement>
        </requirements>
	<command interpreter="Rscript"> $normalizationDESeq </command>
	<inputs>
		<param name="input" type="data" format="tabular" label="Hit lists of items"/>
	</inputs>
	<outputs>
                <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
                <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
	</outputs>
        <tests>
            <test>
                <param name="input" value="counts.tab" ftype="tabular"/>
                <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
                <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
            </test>
        </tests>
  <configfiles>
    <configfile name="normalizationDESeq">
      ## Setup R error handling to go to stderr
      options( show.error.messages=F,  error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
      suppressMessages(require(DESeq))
      countsTable = read.delim("${input}", header=TRUE, check.names=FALSE)
      rownames( countsTable )= countsTable[,1]
      countsTable= countsTable[ , -1 ]
      conds = c(rep ("C", length(countsTable[1,])-1 ), "T")
      cds = newCountDataSet( countsTable, conds )
      cds = estimateSizeFactors( cds )
      write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
      norm_table = as.data.frame(counts( cds, normalized=TRUE ))
      norm_table = cbind(rownames(norm_table), norm_table)
      colnames(norm_table) = c("gene", colnames(countsTable) )
      write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n")
    </configfile>
  </configfiles>
	<help>

**What it does**

DESeq Normalization Factors (geometic mean method)
and
Normalized hit lists

	</help>
</tool>