--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pmlst.xml	Mon Sep 06 18:27:45 2021 +0000
@@ -0,0 +1,68 @@
+<tool id="pmlst" name="pmlst" version="2.0+galaxy2">
+  <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description>
+
+
+  <requirements>
+    <requirement type="package" version="3.2.0">python3-openid</requirement>
+    <requirement type="package" version="21.2.4">pip</requirement>
+    <requirement type="package" version="1.79">biopython</requirement>
+    <requirement type="package" version="1.5.6">cgecore</requirement>
+    <requirement type="package" version="0.8.9">tabulate</requirement>
+    <requirement type="package" version="2.7.1">blastn</requirement>
+  </requirements>
+
+
+  <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output  </command>-->
+
+  <!--<command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>--> 
+
+  <command detect_errors="aggressive"><![CDATA[
+
+#import re
+        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
+        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
+       
+        ## Add single quotes around each input file identifier
+        #set $_input_file = "'{}'".format($input.element_identifier)
+        ln -s '${input}' ${_input_file} &&
+       
+
+        perl $__tool_directory__/pmlst.pl $__tool_directory__ $_input_file $s > $output
+
+
+
+]]></command>
+
+  <inputs>
+	  <param format="fasta" name="input" type="data" label="Select FASTA files: " />
+	  
+
+	  <param name="s" type="select" label="Scheme database used for pMLST prediction:">
+
+	    <option value="incac">incac</option>
+	    <option value="incf">incf</option>
+	    <option value="inchi1">inchi1</option>
+	    <option value="inchi2">inchi2</option>
+	    <option value="inci1">inci1</option>
+	    <option value="incn">incn</option>
+	    <option value="pbssb1-family">pbssb1-family</option>
+	     
+          </param>
+
+	   
+ </inputs>
+
+ <outputs>	 
+    <data format="tabular" name="output" />
+ </outputs>
+
+  <help>
+  
+  </help>
+  <citations>
+	  <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
+	        </citations> 
+</tool>
+
+
+