comparison macros.xml @ 15:bf28a8cff401 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af
author bgruening
date Wed, 20 Mar 2024 07:34:52 +0000
parents 6f28e90db932
children 8e649f27aa0d
comparison
equal deleted inserted replaced
14:6f28e90db932 15:bf28a8cff401
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">7.508</token> 3 <token name="@TOOL_VERSION@">7.520</token>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">22.01</token> 5 <token name="@PROFILE@">22.01</token>
6 <!-- currently, the fasta3 executable is named according to its major version
7 => needs updating together with the package requirement! -->
8 <token name="@FASTA3_EXEC@">fasta36</token>
6 <xml name="biotools"> 9 <xml name="biotools">
7 <xrefs> 10 <xrefs>
8 <xref type="bio.tools">MAFFT</xref> 11 <xref type="bio.tools">MAFFT</xref>
9 </xrefs> 12 </xrefs>
10 </xml> 13 </xml>
11 <xml name="requirements"> 14 <xml name="requirements">
12 <requirements> 15 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">mafft</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">mafft</requirement>
14 <requirement type="package" version="36.3.8">fasta3</requirement> 17 <requirement type="package" version="36.3.8">fasta3</requirement>
15 </requirements> 18 </requirements>
19 </xml>
20 <xml name="weighti_param">
21 <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
22 </xml>
23 <xml name="parttree_parameters">
24 <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/>
25 <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/>
26 <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."/>
27 </xml>
28 <xml name="misc_scoring_scheme">
29 <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" />
30 <conditional name="gap_costs">
31 <param name="use_defaults" type="select" label="Configure gap costs">
32 <option value="yes">Use default values</option>
33 <option value="no">Set values</option>
34 </param>
35 <when value="yes"/>
36 <when value="no">
37 <param argument="--ep" type="float" value="0.0" label="Gap extension penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment."/>
38 <param argument="--op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value"/>
39 </when>
40 </conditional>
41 </xml>
42 <xml name="global_align_options">
43 <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true">
44 <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."/>
45 <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."/>
46 </section>
16 </xml> 47 </xml>
17 <xml name="citations"> 48 <xml name="citations">
18 <citations> 49 <citations>
19 <citation type="doi">10.1093/molbev/mst010</citation> 50 <citation type="doi">10.1093/nar/gkf436</citation>
20 </citations> 51 <citation type="doi">10.1093/nar/gki198</citation>
52 <citation type="doi">10.1093/molbev/mst010</citation>
53 </citations>
21 </xml> 54 </xml>
22 </macros> 55 </macros>