--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MIRUReader.xml	Tue Aug 17 19:15:15 2021 +0000
@@ -0,0 +1,56 @@
+<tool id="mirutool" name="mirureader" version="6.6.0">
+<description> MIRUReader.... </description>
+
+<requirements>
+	<requirement type="package" version="3.2.0">python3-openid</requirement>
+  <requirement type="package" version="6.6.0">emboss</requirement>
+  <requirement type="package" version="1.3.2">pandas</requirement>
+</requirements>
+
+<command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p name 1> $output 2>$logfile</command>
+<!--
+     <command interpreter="bash" 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
+    
+        #for $element in $named_input_files
+            sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $element '-p' $element > $output
+        #end for
+      
+
+
+]]></command>
+-->
+
+<!-- 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  -->
+
+<inputs>
+	<!--
+	<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"/>
+</inputs>
+
+<outputs>
+	<data format="tabular" name="output" label="MIRUreader output"/>
+	<data format="txt" name="logfile" label="Logfile"/>
+</outputs>
+
+<help>
+-Git:https://github.com/phglab/MIRUReader.git
+ </help>
+
+<citations>
+	<citation type="doi">10.1093/bioinformatics/btz771</citation>
+</citations>
+</tool>