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1 <tool id="prep_data" name="PreProcess Expression Data" version="1.3">
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2 <description>Combines gene expression data</description>
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3 <command interpreter="perl">PreProcess_Expression_Data.pl -i $data -c $compslist -a $annot -o $output -p $thresh -l $log -v n</command>
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4 <inputs>
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5 <param format="txt" name="data" type="data" label="Expression data"/>
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6 <param format="txt" name="compslist" type="data" label="Comparison list"/>
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7 <param format="txt" name="annot" type="data" label="Annotation file"/>
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8 <param name="thresh" type="float" min="0" max="1" label="Percentile threshold" value="0.63" optional="true"/>
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9 <param name="log" type="select" label="Log transform data?">
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10 <option value="n" selected="true">No</option>
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11 <option value="y">Yes</option>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="txt" name="output"/>
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16 </outputs>
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17
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18 <tests>
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19 <test>
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20 <param name="data" value="EMBER/expression.txt"/>
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21 <param name="compslist" value="EMBER/comparisons_list.txt"/>
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22 <param name="annot" value="EMBER/annotation.txt"/>
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23 <param name="thresh" value="0.63"/>
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24 <param name="log" value="n"/>
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25 <output name="output" file="EMBER/expression_profiles.txt"/>
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26 </test>
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27 </tests>
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28
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29 <help>
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30
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31 This tool discretizes the gene expression data and adds genomic annotations.
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32
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33 More options for the EMBER tools (especially for the main program, EMBER, including searching for multiple expression patterns) are available in the command line version, available at http://dinner-group.uchicago.edu/downloads.html. That package also includes test data and sample outputs.
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34
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35 When using any of the EMBER tools, please cite: M Maienschein-Cline, J Zhou, KP White, R Sciammas, and AR Dinner. Discovering transcription factor regulatory targets using gene expression and binding data. *Bioinformatics*, 28:206-213 (2012).
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36
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37 -----
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38
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39 Description of inputs:
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40
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41 *Expression Data*:
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42
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43 Microarray data, with data from N experiments (and at least 2 replicates per condition).
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44
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45 *Format (N+1 columns)*: [ID] [expt 1 value] [expt 2 value] ... [expt N value]
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46
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47 IMPORTANT: the first line should be a title line, first field "#ID", and subsequent fields giving the condition/replicate for each column, i.e.,
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48
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49 #ID [condition]#[replicate]...
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50
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51 where [condition] matches the values in the Comparison List, and replicate tells which number the file is. [condition] and [replicate] are delimited by a "#" (so don't use that character in the condition name).
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52
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53 *Comparison List*:
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54
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55 List of behavior dimension definitions. [condition] should match the names in the expression data list.
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56
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57 *Format (2 columns)*: [condition1] [condition2]
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58
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59 *Annotation File*:
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60
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61 Gives the genomic coordinates of each probe set.
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62
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63 *Format (6 columns)*: [probe id] [gene name] [chromosome] [start] [end] [strand]
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64
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65 *Percentile Threshold* (p):
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66
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67 Used to eliminate genes that are consistently expressed at a very low level. All data are concatenated into one list, and the pth percentile of that list is taken as the thresold. Then a probe set is removed if its value is less than the threshold in ALL conditions.
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68
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69 p = 1.0 means all probes are retained, p = 0.0 means none are. However, note that this does NOT necessarily imply that 0.63 means 63% of probe sets are retained.
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70
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71 *Log Transform*: whether or not to take the log of the data before discretization.
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72
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73 </help>
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74
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75 </tool>
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76
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