comparison egapx_runner.xml @ 4:6592ae57bb8b draft

planemo upload for repository https://github.com/ncbi/egapx commit cb2d8304fde9fad4348296c3a51b7992ac5b83bb

3:9b1c2fb3b218

#set econfigfile = $econfig + '.config'
cp  '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
python '$__tool_directory__/ui/egapx.py' '$yamlconfig'  -e '$econfig' -o 'egapx_out']]></command>
  <inputs>
    <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/>
    <param name="econfig" type="select" label="Configuration" help="">
      <option value="docker_minimal">docker minimal only works for the minimal dust mite sample using 6GB and 4 cores</option>
      <option value="singularity">singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommendd</option>
      <option value="docker">docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommend</option>
    </param>
  </inputs>
  <outputs>
    <collection name="egapx_out" type="list" label="Outputs from egapx">
      <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>

4:6592ae57bb8b

#set econfigfile = $econfig + '.config'
cp  '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
python '$__tool_directory__/ui/egapx.py' '$yamlconfig'  -e '$econfig' -o 'egapx_out']]></command>
  <inputs>
    <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/>
    <param name="econfig" type="select" label="Workflow run configuration to suit the machine in use" help="Docker minimal will run the sample minimal dustmite yaml">
      <option value="docker_minimal">Docker_minimal supports only the minimal dust mite example yaml using 6GB and 4 cores</option>
      <option value="singularity">Singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option>
      <option value="docker">Docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option>
    </param>
  </inputs>
  <outputs>
    <collection name="egapx_out" type="list" label="Outputs from egapx">
      <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>