<tool id="deseq2_normalization" name="DESeq2 normalization" version="1.40.2+galaxy1" profile="22.01">
    <description>of hit lists (geometric method)</description>
    <requirements>
      <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command>
    <configfiles>
        <configfile name="normalizationDESeq">
      ## Setup R error handling to go to stderr
      options(show.error.messages =FALSE, error = function(){
          cat(geterrmessage(), file=stderr())
          q("no", 1, FALSE)
          }
      )
      suppressMessages(require(DESeq2))
      countsTable = read.delim("${input}", header = TRUE, check.names = FALSE)
      rownames(countsTable ) = countsTable[,1]
      countsTable = countsTable[, -1]
      conds = factor(c(rep("C", length(countsTable[1, ]) - 1), "T"))
      cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ 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>
    <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>
    <help>

**What it does**

DESeq2_normalization takes a tabular table of raw read counts (integers), each column corresponding to a sample count,
and returns (1) the DESeq2 Size Factors (geometic mean method) and (2) a normalized table (floatting number)
of counts.

**Inputs**

The following table gives an example of the tabular input that has to be provided to the tool:

<![CDATA[

Geneid	Oocyte 1	Oocyte 2	Pronuclei 1	pronuclei 2

NM_001195025	0	0	0	0

NM_028778	0	0	0	0

NM_001290393	0	0	0	0

NM_008922	3133	2276	2288	2659

NM_175370	4	22	7	16

NM_001290390	0	0	0	0

NM_175642	977	1711	1013	459

NM_001290392	0	0	0	0

NM_027671	0	0	0	0

NM_178884	0	0	0	2

NM_199021	332	413	1436	836

NM_198680	0	0	0	0

NM_011465	0	4	0	0

NM_130890	0	0	0	0

NM_001113393	0	0	0	0

NM_001113392	0	0	0	0

NM_001113391	19	3	88	15

NM_031162	0	0	0	0

NR_103716	0	0	0	0

NM_001160371	0	0	0	0

NM_177834	1	3	2	0

NM_145381	606	445	367	306

]]>
    </help>
    <citations>
        <citation type="doi">10.1186/s13059-014-0550-8</citation>
    </citations>
</tool>