<tool id="countdifferences" name="countDifferences tool" version="1.0.0">
  <description>allows to compare sequences from a multi-Fasta alignment file by calculating differences (in bp) and percentage identity</description>

<requirements>
  <requirement type="package" version="1.7.2">perl-bioperl</requirement>
  <!--<requirement type="package" version="3.27">perl-string-approx</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')
            ## Add single quotes around each input file identifier
            #set $_input_file = "'{}'".format($input.element_identifier)
            ln -s '${input}' ${_input_file} &&


        perl '$__tool_directory__/countDifferences.pl' $_input_file $output1 $output2



]]></command>
 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->

<inputs>
  <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
  <!--<param name="char" type="text" area="false" value="N" label="Character to be removed from Multi-FASTA file:" help="Users can directly write the character to be removed without quotes" />-->
</inputs>

 <outputs>
    <data format="tabular" name="output1" label="bp_differences.tsv "/>
    <data format="tabular" name="output2" label="percentage_identity.tsv "/>
 </outputs>

<help><![CDATA[
countDifferences.pl is a Perl script allowing to calculate differences (changes in bp) and sequences percentage identity from an aligned multi-Fasta file.

Two resulting tables are produced:
(i) a table containing a matrix with bp differences for each sequence;
(ii) a table containing a matrix with percentage identity for each sequence

This script belongs to the getSequenceInfo supplementary tools.

- GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
]]>
</help>

</tool>