view consensus.xml @ 0:0cebe436a553 draft default tip

Initial upload.

<tool id="pathprint-consensus" name="Create a Consensus">
  <command>consensus.r $input $threshold $output</command>

  <inputs> 
    <param name="input" type="data" label="Pathway Fingerprint" help="Submit a Pathway Fingerprint file from your history"/> 

    <param name="threshold" type="select" label="Threshold" help="Select a threshold value">
      <option value="0.9">0.9</option>
      <option value="0.8" selected="true">0.8 (default)</option>
      <option value="0.7">0.7</option>
      <option value="0.6">0.6</option>
      <option value="0.5">0.5</option>
    </param>
  </inputs>

  <outputs> 
    <data format="tabular" name="output" label="Consensus Fingerprint"/> 
  </outputs>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

  <help> 

**What it does**

This tool identifies the most prevalent PathPrint value for each pathway across the submitted samples and produces a consensus PathPrint.

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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**Input:** PathPrint fingerprint for multiple samples and a threshold value. 

**Output:** A single consensus PathPrint fingerprint representing the most commonly occurring value

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Feedback is welcome. Please send your questions, comments and suggestions to [e-mail].
  </help>
</tool>