plasmidinfotool.xml

<tool id="plasmidinfo1" name="PlasmidInfo" version="0.1.0">
    <description>Get plasmid list for a given design.</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 $synology:/shared:ro  -e SBCDATA_SHARED=/shared -e DATA=/data sbc1 python /tools/plasmidInfo.py -i $design1 -o $output1 
    ]]></command>
    <inputs>
    	<param name="design1" type="text" label="Design id" value="SBCDE00053" help="SBC design id" />
    	<param name="synology" type="text" label="Synology" value="/SynologyShared" help="Synology shared mount point" />
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out.csv" />
    </outputs>
    <help><![CDATA[
    Plasmid info for a given design.
    
    - Inputs:
        - Design id: SBC design id.
	- Synology

    - Outputs:
        - *csv* file with the list of plasmid ids for the design.
    
.. class:: infomark

Pablo Carbonell, SYNBIOCHEM, University of Manchester, 2020.


	]]></help>
</tool>