<tool id="mirureader" name="mirureader" version="1.0.0">
<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>
  <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 sample 1> $output 2>$logfile</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}" &&   
        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  -->

<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><![CDATA[
MIRUReader allows to identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). It also work on assembled genome.

GitHub: https://github.com/phglab/MIRUReader.git
]]>
</help>

<citations>
<citation type="doi">10.1093/bioinformatics/btz771</citation>
</citations>
</tool>