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<tool id="EBGeneTwoCondTest" name="Gene level DE test across two conditions" version="1.0.1">
  <description>Runs EBSeq to find DE genes across two conditions</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

  <command>R --quiet --slave --file=$__tool_directory__/EBGeneTwoCondTest.R --args $Gene_Expression $First_Row_Sample_Names $Conditions $Target_FDR $Output $Sorted_Output $Sorted_Output_with_target_FDR $Sizes 1>NUL 2>NUL</command>
  <inputs>
		<param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab delimited, please use the unnormalized values, e.g. expected counts from RSEM)"/>
		<param name="First_Row_Sample_Names" type="select" format="text">
			<label>The First Row is Sample Names?</label>
			<option value="y">Yes</option>
			<option value="n">No</option>
			</param>
		<param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each
			sample belongs to (separated by comma, no space please)." 
			help="Sample with condition that comes first alphabetically will be in numerator (C1 relative to C2)."/>
		<param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR"
			/>
  </inputs>
  <outputs>
		<data format="tabular" name="Output" label="Output"/>
		<data format="tabular" name="Sorted_Output" label="Output sorted by PPDE"/>
		<data format="tabular" name="Sorted_Output_with_target_FDR" label="Sorted output with FDR cutoff"/>
                <data format="tabular" name="Sizes" label="Normalization factors"/>
  </outputs>

  <help>
The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of 
columns in the data file (except the gene names column).

Four output files will be generated. Each of the first 3 files contains Posterior probability of being 
DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized gene expressions.
The Four files are:
Genes with the same order as in input file;
Genes sorted by PPDE; DE Genes under target FDR (PPDE>=TargetFDR) 
and sorted by PPDE;
Library size factor for each sample.

</help>

    <expand macro="citation" />

</tool>