view egapx_runner.xml @ 1:c8e1543546f8 draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4-dirty

<tool name="egapx_runner" id="egapx_runner" version="6.0.1" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 03/08/2024 10:40:32 using the Galaxy Tool Factory.-->
  <description>Runs egapx</description>
  <requirements>
    <requirement version="3.12.3" type="package">python</requirement>
    <requirement version="24.04.4-0" type="package">nextflow</requirement>
    <requirement version="6.0.1" type="package">pyyaml</requirement>
  </requirements>
  <version_command><![CDATA[echo "6.0.1"]]></version_command>
  <command><![CDATA[mkdir -p ./egapx_config &&
#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"/>
    </collection>
  </outputs>
  

<tests>
    <test>
      <output_collection name="egapx_out" count="8"/>
      <param name="yamlconfig" value="yamlconfig_sample"/>
      <param name="econfig" value="docker_minimal"/>
    </test>
</tests>



  <help><![CDATA[
 **What it Does**
  ]]></help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/bts573</citation>
  </citations>
</tool>