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diff clsi_profile.xml @ 0:62226cd1acb5 draft

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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
author rakesh4osdd
date Fri, 11 Jun 2021 12:36:25 +0000
parents
children 683299422575
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi_profile.xml	Fri Jun 11 12:36:25 2021 +0000
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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>