view synapseGetDataset.xml @ 46:ebf3bc09c383

add snpEff code

<tool id="synapseGetDataset" description="Get a specified dataset and metadata from Synapse" name="Get Synapse Data" version="0.0.1">
  <description>
    Retrieve a dataset from Synapse
  </description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    synapseGetDataset.py $synapseId $username $metadataFile $dataFile
    #if $loginType.type == "password"
        --password $loginType.password
    #else
        --apiKey $loginType.apiKey
    #end if
  </command>
  <inputs>
    <param type="text" name="synapseId" label="Synapse ID" optional="false"/>
    <param type="text" name="username" label="Synapse Username or Email" optional="false">
      <sanitizer sanitize="False"/>
    </param>
    <conditional name="loginType">
      <param type="select" name="type" label="Login Type">
	<option value="apiKey">Email Address and API Key (Recommended)</option>
	<option value="password">Email Address and Password</option>
      </param>
      <when value="password">
	<param type="text" name="password" label="Password" optional="false">
	  <sanitizer sanitize="False"/>
	</param>
      </when>
      <when value="apiKey">
	<param type="text" name="apiKey" label="API Key" optional="false">
	  <sanitizer sanitize="False"/>
	</param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="txt" name="metadataFile" label="${synapseId}.json"/>
    <data format="tabular" name="dataFile" label="${synapseId}" />
  </outputs>
  <help>
    This module downloads a dataset from Synapse, given the Synapse ID of the dataset and user authentication.  The user authentication can take one of two forms: email address and Synapse password, or email address and Synapse API key.  We recommend logging in with the email address and Synapse API key, for greater security.  The Synapse API key is specific to each user, and is available from the Synapse Settings page.

    Note that this module is limited to single-file Synapse datasets.  Synapse Projects and Folders must be downloaded with a separate mechanism.
  </help>
</tool>