diff macros.xml @ 16:8e649f27aa0d draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443

--- a/macros.xml	Wed Mar 20 07:34:52 2024 +0000
+++ b/macros.xml	Thu Aug 22 19:20:24 2024 +0000
@@ -1,6 +1,5 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">7.520</token>
+    <token name="@TOOL_VERSION@">7.526</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <!-- currently, the fasta3 executable is named according to its major version
@@ -18,15 +17,15 @@
         </requirements>
     </xml>
     <xml name="weighti_param">
-        <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
+        <param argument="--weighti" type="float" min="1" max="100" value="2.7" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
     </xml>
     <xml name="parttree_parameters">
-        <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/>
-        <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/>
-        <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
+        <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is built this number of times in the progressive stage."/>
+        <param argument="--partsize" type="integer" min="0" max="1000" value="50" label="Number of partitions in the PartTree algorithm."/>
+        <param argument="--groupsize" type="integer" min="-1" value="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
     </xml>
     <xml name="misc_scoring_scheme">
-        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" />
+        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?"/>
         <conditional name="gap_costs">
             <param name="use_defaults" type="select" label="Configure gap costs">
                 <option value="yes">Use default values</option>
@@ -42,7 +41,7 @@
     <xml name="global_align_options">
         <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true">
             <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/>
-            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/>
+            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for &gt; ~1000 sequences."/>
         </section>
     </xml>
     <xml name="citations">