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1 <tool id="integrate_data" name="Integrate Data" version="1.3">
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2 <description>Assigns potential targets to binding sites</description>
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3 <command interpreter="perl">Integrate_Data.pl -b $binding_data -e $expression_data -o $output -d $dist -dt $dtype -v n</command>
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4 <inputs>
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5 <param format="txt" name="binding_data" type="data" label="Binding data"/>
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6 <param format="txt" name="expression_data" type="data" label="Discretized expression data"/>
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7 <param name="dist" type="integer" min="0" label="Max distance (kbp)" value="100" optional="true"/>
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8 <param name="dtype" type="select" label="Distance type">
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9 <option value="1" selected="true">To gene boundaries</option>
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10 <option value="2">To TSS</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="output"/>
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15 </outputs>
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16
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17 <tests>
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18 <test>
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19 <param name="binding_data" value="EMBER/peaks.txt"/>
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20 <param name="expression_data" value="EMBER/expression_profiles.txt"/>
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21 <param name="dist" value="100"/>
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22 <param name="dtype" value="1"/>
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23 <output name="output" file="EMBER/integrated.txt"/>
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24 </test>
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25 </tests>
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26
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27 <help>
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28
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29 This tool combines binding data with annotated gene/probe sets to assign potential targets to each binding site.
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30
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31 -----
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32
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33 Description of inputs:
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34
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35 *Binding Data*:
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36
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37 Binding data in bed-like format (note only the first coordinate after [chr] is used, so if you have the regular bed format, you may want to add a new second column with the average of the start and end coordinates). [other information] is retained throughout the analysis, and may contain peak ID, peak enrichment, etc.
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38
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39 *Format (at least 2 columns)*: [chr] [peak posn] [other information]
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40
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41 *Discretized Expression Data*: output of PreProcess Expression Data.
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42
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43 *Max Distance*: maximum distance from a peak in order to consider a gene a potential target (in kbp).
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44
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45 *Distance Type*: definition of distance (to gene boundaries or to TSS). If "To gene boundaries" is chosen, peaks lying within a gene's coordinates have a distance of 0.
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46
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47 </help>
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48
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49 </tool>
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50
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