diff clsi_profile.xml @ 3:683299422575 draft

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"

--- a/clsi_profile.xml	Fri Jun 11 13:20:08 2021 +0000
+++ b/clsi_profile.xml	Tue Jun 29 05:20:41 2021 +0000
@@ -21,7 +21,7 @@
    		</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>
+				<option value="test-data/clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
    			</param>
    		</when>
    		<when value="user_file">
@@ -45,6 +45,40 @@
         </test>
     </tests>
     <help><![CDATA[
-        TODO: Fill in help.
+        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>