--- a/MIRUReader.xml	Tue Aug 17 23:27:22 2021 +0000
+++ b/MIRUReader.xml	Fri Sep 03 19:52:01 2021 +0000
@@ -1,5 +1,5 @@
 <tool id="mirureader" name="mirureader" version="1.0.0">
-<description> MIRUReader allows to perform in-silico MIRU-VNTR typing using long reads or assembled genome </description>
+<description> MIRUReader allows to perform in-silico MIRU-VNTR typing using assembled genomes (FASTA format)</description>
 
 <requirements>
 <requirement type="package" version="3.2.0">python3-openid</requirement>
@@ -17,16 +17,22 @@
   
         ## Add single quotes around each input file identifier
         #set $_input_file = "'{}'".format($input.element_identifier)
-        #set $_input_file = $_input_file + '.fasta'
-        ln -s '${input}' ${_input_file} &&   
-    
-        python3 $__tool_directory__/MIRUReader/MIRUReader.py -r $_input_file -p $_input_file > $output
+        
+       
+        ln -s '${input}' "${_input_file}" &&   
+        cp "$_input_file" input.fasta &&
+        python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p $_input_file > $output
         
       
 
 
 ]]></command>
 
+<!--   #set $var = ${_input_file//[^[:alnum:]]/}
+#set var = ${f//:()/}
+ #set $_input_file = $_input_file + '.fasta' 
+$_input_file="${_input_file// /_}" &&  -->
+
 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output 
 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output  -->
 
@@ -34,7 +40,7 @@
 <!--
 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
 -->
-       <param format="fasta" name="input" type="data" label="Fasta file"/>
+       <param format="fasta" name="input" type="data" label="FASTA file"/>
 </inputs>
 
 <outputs>