Mercurial > repos > iuc > pal2nal

diff macros.xml @ 0:a14d5c1e1fc4 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 10:56:21 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Nov 09 10:56:21 2025 +0000
@@ -0,0 +1,39 @@
+<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>