plasmidwriter.xml

<tool id="plasmidwriter" name="PlasmidWriter" version="0.1.0">
    <description>Write plasmids in ICE.</description>
    <command detect_errors="exit_code"><![CDATA[
  docker run -v $__tool_directory__:/tools -v /export/galaxy-central/database/files:/export/galaxy-central/database/files:rw -v /export/galaxy-central/database/job_working_directory:/export/galaxy-central/database/job_working_directory:rw -w /tools/code/PartsGenie -e PYTHONPATH=:/tools/code/PartsGenie sbc1 python scripts/plasmid_writer.py $input1 $output1 $ice.server $ice.username $ice.pass $ice.group 
    ]]></command>
    <inputs>
      <param name="input1" type="data" label="Plasmid list" help="Plasmid list" format="csv"/>
    <section name="ice" title="ICE Options" expanded="false">
      <param name="server" type="text" label="ICE Server" help="ICE registry server"
	     value="https://ice.synbiochem.co.uk"/>
      <param name="username" type="text" label="ICE User" help="ICE user name">
	<sanitizer invalid_char="">
	  <valid initial="string.ascii_letters,string.digits,string.punctuation">
	    <add value="_" />
	  </valid>
	</sanitizer>
      </param>
      <param name="pass" type="text" label="ICE Pass" help="ICE login"/>
      <sanitizer invalid_char="">
	<valid initial="string.ascii_letters,string.digits,string.punctuation">
	  <add value="_" />
	</valid>
      </sanitizer>
      <param name="group" type="text" label="ICE Group" help="ICE Group" value="synbiochem"/>
    </section>
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out.csv" />
    </outputs>
    <help><![CDATA[
    Plasmid writer tool.
    
    Inputs:

       - Plasmids list: csv file with columns part,vector.
       - ICE details

    Outputs:
       - CSV file with plasmids details.
    
    ]]></help>
</tool>