--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP.xml	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,38 @@
+<tool id="PGAP" name="PGAP" version="1.0">
+  <description>Pan-Genome Analysis Pipeline </description>
+  <requirements>
+	 <requirement type="package" version="2.11.0">blast</requirement>
+	 <requirement type="package" version="7.480">mafft</requirement>
+	 <requirement type="package" version="14.137">mcl</requirement>
+	 <requirement type="package" version="3.697">phylip</requirement>
+	 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
+</requirements> -->
+    <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')
+        #set $named_input_files = ''
+        #for $input_file in $input_files
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input_file.element_identifier)
+            ln -s '${input_file}' ${_input_file} &&
+            #set $named_input_files = $named_input_files + ',' + $_input_file
+        #end for
+
+	perl ${__tool_directory__}/PGAP_wrapper2.pl -g $input_files -p $proteins -o $named_input_files -o $output	
+	]]></command>
+
+
+
+  <inputs>
+	  <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/>
+	  <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/>
+ </inputs>
+
+ <outputs>
+	 <data format="txt" name="output" label="Pangenome presence absence matrix"/>
+
+</outputs>
+
+</tool>