view clsi_profile.xml @ 2:306236ec0511 draft

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<tool id="clsi_profile" name="CLSI Profile" version="0.1.6" 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="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[
        TODO: Fill in help.
    ]]></help>
</tool>