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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:21 +0000
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<macros>
    <xml name="version_command">
        <version_command>pal2nal.pl | head -n 1</version_command>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">pal2nal</requirement>
        </requirements>
    </xml>
    <xml name="command">
        <command detect_errors="exit_code"><![CDATA[
pal2nal.pl '$protein_alignment'
#for $nuc in $nucleotide_fastas:
  '$nuc'
#end for
  -output $output_format
  $show_only_blocks
  $remove_gaps
  $remove_mismatches
  -codontable $genetic_code
  $suppress_stderr
  > '$output_file';
#if $html_output:
pal2nal.pl '$protein_alignment'
#for $nuc in $nucleotide_fastas:
  '$nuc'
#end for
  -output $output_format
  $show_only_blocks
  $remove_gaps
  $remove_mismatches
  -codontable $genetic_code
  -html
  $suppress_stderr
  > '$html_output_file'
#end if
        ]]></command>
    </xml>
</macros>