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

Initial upload.

<tool id="pathprint-distance" name="Find Distance to Pluripotent Signature">

<!--
<description>Find Distance to Pluripotent Signature</description>
-->

  <command>distance.r $input $output $output2</command>

  <inputs> 
    <param name="input" type="data" label="Pathway Fingerprint" help="Submit a PathPrint Fingerprint file from your history to determine how similar your experiment is to pluripotent samples in GEO"/> 
  </inputs>

  <outputs> 
    <data format="tabular" name="output" label="Distance from pluripotent consensus"/>
    <data format="pdf" name="output2" label="Histogram"/> 
  </outputs>

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

  <help> 

**What it does**

This tool takes the computed PathPrint Fingerprint as input and uses it to determine how similar
your data are to a consensus signature generated from a set of pluripotent samples in GEO. 

-----

**Input**: A PathPrint Fingerprint file from your history

**Output**: 

1. Distance from pluripotent consensus: tab delimited file containing distance and p-value for each sample from the pluripotent consensus signature.

2. Histogram: PDF file containing two histograms: (1) distribution of distances for ~180,000 GEO samples from the pluripotent signature; (2) distribution of distances for the input samples from the pluripotent signature.

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