lcr2tool_docker.xml

<tool id="lcr2tool_docker" name="LCR2Tool" version="0.1.0">
  <requirements>
    <container type="docker">sbc1</container>
  </requirements>
    <description>generate work list from list of plasmids TO DO: Select plates.</description>
    <command detect_errors="exit_code"><![CDATA[
            python3 $__tool_directory__/lcr2Tool.py -plasmids $input1 -output $output1 -tempFolder $output1.extra_files_path
        #for $q in $queries2
            -plates ${q.input3}
        #end for

    ]]></command>
    <inputs>
    	<param name="input1" type="data" label="Plasmids" help="Plasmid csv file" format="csv"/>
        <repeat name="queries2" title="Plate files">
            <param name="input3" type="data" label="Plate file" format="csv" />
        </repeat>
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out.csv" />
    </outputs>
    <help><![CDATA[
    LCR tool: generate work list generation for Ligase Cycling Reaction (LCR) from list of plasmids 

    - Inputs:
            - Plasmids: *csv* file(s) with the list(s) of plasmids.
            - Plate files: *csv* or *xlsx* file(s) with plate information. **Feature not implemented**

    - Outputs:
        - *csv* file with the merged list of primers.
    
.. class:: infomark

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