annotate clsi_profile.xml @ 5:3c27e5c2a8e9 draft

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"

<tool id="clsi_profile" name="CLSI Profile" version="0.1.7" python_template_version="3.5">
    <description>MIC profile using CLSI MIC breakpoints</description>
    <requirements>
        <requirement type="package">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
	#if $input2.type_selector == "clsi_file"
		python "${__tool_directory__}/clsi_profile.py" "$input1" "${__tool_directory__}/$input2.clsi1" "$output1"
	#else
		python "${__tool_directory__}/clsi_profile.py" "$input1" "$input2.clsi2" "$output1"
	#end if
    ]]></command>
    <inputs>
   	
   	<param name="input1" type="data" format="csv" label="Input file of Antimicrobial Susceptibility Testing (AST) MIC values for strains" help="Input AST file in CSV format (Please see example given below)"></param>
   	
   	<conditional name="input2">
   		<param name="type_selector" type="select" label="Choose MIC Breakpoints">
   			<option value="clsi_file">CLSI MIC breakpoints</option>
   			<option value="user_file" >User define MIC breakpoints</option>
   		</param>
   		<when value="clsi_file">
   			<param name="clsi1" type="select" format="csv" label="CSV File">
				<option value="test-data/clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
   			</param>
   		</when>
   		<when value="user_file">
   			<param name="clsi2" type="data" format="csv" label="CSV File"></param>
   		</when>
	</conditional>
   	
    </inputs> 
    <!--inputs>
        <param type="data" name="input1" format="csv" />
        <param type="data" name="input2" format="csv" />
    </inputs-->
    <outputs>
        <data name="output1" format="csv" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.csv"/>
            <param name="input2" value="clsi.csv"/>
            <output name="output1" file="output.csv"/>
        </test>
    </tests>
    <help><![CDATA[
        Input CSV file example:
	    Strain name,Antibiotics,MIC,unit

	    Acinetobacter baumannii A85,Colistin,0.1,mg/L
	   
	    Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,1,mg/L

	    Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,8,mg/L

	    Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,4,mg/L

	    Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid, 16/8,mg/L

	Output CSV file example:
	    Strain name,Colistin,Polymyxin B

	    Acinetobacter baumannii A85,Strain could not be classified,NA

	    Acinetobacter baumannii strain FDA-CDC-AR_0306,NA,Strain could not be classified

	    Acinetobacter baumannii strain FDA-CDC-AR_0307,NA,Resistant

	    Acinetobacter baumannii strain FDA-CDC-AR_0308,NA,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>