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1 <tool id="pathprint-consensus" name="Create a Consensus">
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2 <command>consensus.r $input $threshold $output</command>
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3
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4 <inputs>
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5 <param name="input" type="data" label="Pathway Fingerprint" help="Submit a Pathway Fingerprint file from your history"/>
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6
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7 <param name="threshold" type="select" label="Threshold" help="Select a threshold value">
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8 <option value="0.9">0.9</option>
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9 <option value="0.8" selected="true">0.8 (default)</option>
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10 <option value="0.7">0.7</option>
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11 <option value="0.6">0.6</option>
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12 <option value="0.5">0.5</option>
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13 </param>
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14 </inputs>
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15
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16 <outputs>
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17 <data format="tabular" name="output" label="Consensus Fingerprint"/>
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18 </outputs>
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19
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20 <stdio>
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21 <exit_code range="1:" level="fatal" />
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22 </stdio>
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23
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24 <help>
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25
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26 **What it does**
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27
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28 This tool identifies the most prevalent PathPrint value for each pathway across the submitted samples and produces a consensus PathPrint.
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29
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30 The method calculates the mean value of the pathway activities across samples, and then applies the threshold such that if the mean is greater than threshold, the pathway is assigned a consensus of +1. If the mean is less than -threshold, a value of -1 is assigned. Otherwise, the consensus is assigned a value of 0.
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31
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32 -----
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33
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34 **Input:** PathPrint fingerprint for multiple samples and a threshold value.
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35
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36 **Output:** A single consensus PathPrint fingerprint representing the most commonly occurring value
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37
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38 -----
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39
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40 Feedback is welcome. Please send your questions, comments and suggestions to scde@hsci.harvard.edu.
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41 </help>
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42 </tool>
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43
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