<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>