<tool id="removechar" name="removeChar tool" version="1.0.0">
  <description>allows to remove positions (or columns) from a multi-Fasta alignment file in function of a given character</description>

<!--<requirements>
  <requirement type="package" version="1.7.2">perl-bioperl</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__/removeChar.pl' $_input_file $char > "$output"



]]></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="fasta" name="output" />
 </outputs>

<help><![CDATA[
removeChar.pl is a Perl script allowing to remove positions (or columns) of an aligned multi-Fasta file in function of a given character (eg. N).
The resulting multi-Fasta file corresponds to the same input multiFasta alignment file without the queried character.

This script belongs to the getSequenceInfo supplementary tools.

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

</tool>