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1 <tool id="EBGeneTwoCondTest" name="Gene level DE test across two conditions" version="1.0.1">
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2 <description>Runs EBSeq to find DE genes across two conditions</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10
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11 <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>
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12 <inputs>
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13 <param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab delimited, please use the unnormalized values, e.g. expected counts from RSEM)"/>
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14 <param name="First_Row_Sample_Names" type="select" format="text">
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15 <label>The First Row is Sample Names?</label>
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16 <option value="y">Yes</option>
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17 <option value="n">No</option>
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18 </param>
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19 <param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each
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20 sample belongs to (separated by comma, no space please)."
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21 help="Sample with condition that comes first alphabetically will be in numerator (C1 relative to C2)."/>
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22 <param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR"
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23 />
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="Output" label="Output"/>
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27 <data format="tabular" name="Sorted_Output" label="Output sorted by PPDE"/>
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28 <data format="tabular" name="Sorted_Output_with_target_FDR" label="Sorted output with FDR cutoff"/>
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29 <data format="tabular" name="Sizes" label="Normalization factors"/>
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30 </outputs>
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31
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32 <help>
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33 The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of
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34 columns in the data file (except the gene names column).
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35
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36 Four output files will be generated. Each of the first 3 files contains Posterior probability of being
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37 DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized gene expressions.
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38 The Four files are:
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39 Genes with the same order as in input file;
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40 Genes sorted by PPDE; DE Genes under target FDR (PPDE>=TargetFDR)
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41 and sorted by PPDE;
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42 Library size factor for each sample.
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43
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44 </help>
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45
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46 <expand macro="citation" />
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47
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48 </tool>
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