asist.xml

<tool id="asist" name="ASIST" version="1.0.1" python_template_version="3.5">
    <description>Antimicrobial Susceptibility standards based phenotypes</description>
    <requirements>
        <requirement type="package">pandas</requirement>
    </requirements>
    <version_command>python -c "import pandas; print(pandas.__version__)"</version_command>
    <command detect_errors="exit_code"><![CDATA[
	    "python ${__tool_directory__}/asist_dynamic.py" "$input1" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="csv" />
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="test-data/asist_output.csv" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test-data/asist_input.csv"/>
            <output name="output1" file="test-data/asist_output.csv"/>
        </test>
    </tests>
    <help><![CDATA[
        Input CSV file example:
	    Strain name,Amikacin,Tobramycin,Gentamycin,Imipenem
	    Strain name,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems
	    Acinetobacter baumannii strain FDA-CDC-AR_0288,Resistant,Resistant,Resistant,Resistant
	    Acinetobacter baumannii strain FDA-CDC-AR_0303,Resistant,Resistant,Resistant,Resistant
	    Acinetobacter baumannii strain FDA-CDC-AR_0304,NA,Resistant,Resistant,Resistant
	Output CSV file example:
	    Strain name,Strain phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem
	    Strain name,Strain could not be classified,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems
	    Acinetobacter baumannii strain FDA-CDC-AR_0288,Strain could not be classified,Resistant,Resistant,Resistant,Resistant
	    Acinetobacter baumannii strain FDA-CDC-AR_0303,Strain could not be classified,Resistant,Resistant,Resistant,Resistant
	    Acinetobacter baumannii strain FDA-CDC-AR_0304,Strain could not be classified,NA,Resistant,Resistant,Resistant
    ]]></help>
    <citations>
	    <citation type="bibtex">@ARTICLE{Sharma_2021,
		    	author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj},
		    	title = {ASIST: Antimicrobial Susceptibility standards based phenotypes},
		    	journal = {},
		        year = {2021},
		    	volume = {},
		    	pages = {},
		    	url = {https://ab-openlab.csir.res.in/asist}
		    }
	    </citation>
    </citations>
</tool>