Mercurial > repos > iuc > pal2nal
comparison macros.xml @ 0:a2a40f3bfbbd draft default tip
planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
| author | iuc |
|---|---|
| date | Sun, 09 Nov 2025 10:56:06 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:a2a40f3bfbbd |
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| 1 <macros> | |
| 2 <xml name="version_command"> | |
| 3 <version_command>pal2nal.pl | head -n 1</version_command> | |
| 4 </xml> | |
| 5 <xml name="requirements"> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@TOOL_VERSION@">pal2nal</requirement> | |
| 8 </requirements> | |
| 9 </xml> | |
| 10 <xml name="command"> | |
| 11 <command detect_errors="exit_code"><![CDATA[ | |
| 12 pal2nal.pl '$protein_alignment' | |
| 13 #for $nuc in $nucleotide_fastas: | |
| 14 '$nuc' | |
| 15 #end for | |
| 16 -output $output_format | |
| 17 $show_only_blocks | |
| 18 $remove_gaps | |
| 19 $remove_mismatches | |
| 20 -codontable $genetic_code | |
| 21 $suppress_stderr | |
| 22 > '$output_file'; | |
| 23 #if $html_output: | |
| 24 pal2nal.pl '$protein_alignment' | |
| 25 #for $nuc in $nucleotide_fastas: | |
| 26 '$nuc' | |
| 27 #end for | |
| 28 -output $output_format | |
| 29 $show_only_blocks | |
| 30 $remove_gaps | |
| 31 $remove_mismatches | |
| 32 -codontable $genetic_code | |
| 33 -html | |
| 34 $suppress_stderr | |
| 35 > '$html_output_file' | |
| 36 #end if | |
| 37 ]]></command> | |
| 38 </xml> | |
| 39 </macros> |