view put_dataset.xml @ 0:7698311d4466 draft

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<tool id="hadoop_galaxy_put_dataset" name="Put dataset" version="0.1.0">
  <description>Copy data from Galaxy storage to Hadoop storage.</description>
  <requirements>
    <requirement type="package" version="0.11">pydoop</requirement>
    <requirement type="package" version="0.1.1">hadoop-galaxy</requirement>
  </requirements>

  <command>
    put_dataset
    #if $workspace != ""
      --hadoop-workspace "$workspace"
    #end if
    #if $use_distcp
      --distcp
    #end if
    "$input_pathset" "$output_path"
  </command>

  <inputs>
    <param name="input_pathset" type="data" format="pathset" label="Galaxy pathset" />

    <param name="workspace" type="text" label="Path to workspace for Hadoop data"
       help="The data will be copied to a new directory under this path. The value can also be set through the HADOOP_GALAXY_PUT_DIR environment variable." />

    <param name="use_distcp" type="boolean" checked="false" label="Use Hadoop distcp2"
       help="Use distcp2 if Hadoop can access Galaxy's storage space and you're copying a large dataset." />
  </inputs>

  <outputs>
    <data name="output_path" format="pathset" label="Hadoop pathset from $input_pathset.name" />
  </outputs>

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

  <help>
      This tools copies data from Galaxy's storage to storage that is suitable for
      Hadoop jobs.  An example of a use case may be to copy data from the Galaxy server
      to HDFS. Whether this tool is required depends on your specific local setup.
  </help>

</tool>