plasmidgenietool.xml

<tool id="plasmidgenietool" name="PlasmidGenie" version="0.1.0">
  <description>Generate order list for parts and oligos and plasmids list from constructs.</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 -v $__tool_directory__/data:/data -v $__tool_data_path__:/tmp  -e PLASMID_GENIE_PATH=/tools/code/PlasmidGenieClient -e DATA=/data -e ICE_SERVER=$ice.input2 -e ICE_USERNAME=$ice.input3 -e ICE_PASSWORD=$ice.input4 -e ICE_GROUP=$ice.input6 -e INPUT=$input1 -e OUTPUT1=$output1 -e OUTPUT2=$output2 sbc1 sh /tools/plasmidgenie_job.sh 
  ]]></command>
  <inputs>
    <param name="input1" type="data" label="Constructs" help="Plasmid csv file" format="txt"/>
    <param name="input5" type="text" label="Restriction enzymes" value="MlyI"
	   help="Comma separated restriction enzymes" />
    <section name="ice" title="ICE Options" expanded="false">
      <param name="input2" type="text" label="ICE Server" help="ICE registry server"
	     value="https://ice.synbiochem.co.uk"/>
      <param name="input3" 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="input4" 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="input6" type="text" label="ICE Group" help="ICE Group" value="synbiochem"/>
    </section>
  </inputs>
  <outputs>
    <data name="output1" format="csv" label="Order list for ${input1.name}" />
    <data name="output2" format="csv" label="Plasmid file for ${input1.name}" />
  </outputs>
  <environment_variables>
    <environment_variable name="PYTHONPATH">$__tool_directory__/code/PlasmidGenieClient</environment_variable>
  </environment_variables>
    <help><![CDATA[
    PlasmidGenie: generate plasmids, parts and oligos list for a given combinatorial library.

    Inputs:

    - Plasmids: txt file generated by DoE.
    - Restriction enzymes: comma separated restriction enzymes.
    - ICE details.

    Outputs:
    
    - zip file with parts list and plasmid mapping.
    
.. class:: infomark

Pablo Carbonell, SYNBIOCHEM, University of Manchester, 2020.
    ]]></help>
</tool>