cpo_rgi.xml

<tool id="cpo_rgi" name="cpo_rgi" version="4.0.3">
  <description>Modified version of RGI to make it support galaxy without using a datatable by using the --local flag</description>
  <requirements>
        <requirement type="package" version="4.0.3">rgi</requirement>
		<requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        rgi load -i $__tool_directory__/databases/card202.json --local && rgi main -t contig -a BLAST -i $input -o rgiResult -n "\${GALAXY_SLOTS:-4}" --local --clean 
    ]]></command>

    <inputs>
        <param type="data" name="input" format="fasta" />
    </inputs>
    <outputs>
		<data name="rgiResultTsv" format="tabular" from_work_dir="rgiResult.txt"/>
    </outputs>
    <help>
		runs rgi with the --local flag due to improper galaxy support with existing rgi. requires a card.json database in the databses folder. 
	</help>
	<citations>
	<citation type="bibtex">
@misc{cpo,
  author = {j, j},
  year = {2018},
  title = {cpo_prediction},
  publisher = {j},
  journal = {j of j},
  url = {https://bfjia.net,
}</citation>
    </citations>
</tool>