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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
author iuc
date Sun, 21 Dec 2025 10:17:03 +0000
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21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
1 <tool id="raxmlng" name="RAxML-NG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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2 <description>Maximum Likelihood based inference of large phylogenetic trees</description>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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3 <macros>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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4 <token name="@TOOL_VERSION@">1.2.2</token>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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6 </macros>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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7 <xrefs>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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8 <xref type="bio.tools">RAxML-NG</xref>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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9 </xrefs>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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10 <requirements>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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11 <requirement type="package" version="@TOOL_VERSION@">raxml-ng</requirement>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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12 </requirements>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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13 <command detect_errors="exit_code"><![CDATA[
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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14 raxml-ng
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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15 $command
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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16 #if $command == '--consense':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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17 $consensus_type
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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18 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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19 --msa '$infile'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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20 --prefix galaxy
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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21 #if $model.model_type == 'single_gui':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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22 #if $model.seq_type == 'multistate':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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23 #set model_matrix = '""'.join(["MULTI", str($model.single_model.multi_state_count),"_",str($model.single_model.subst_matrix)])
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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24 #else:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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25 #set model_matrix = str($model.single_model.subst_matrix)
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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26 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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27 #if str($model.rhas_model) in ['+G', '+R', '+I+G', '+I+R']:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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28 #set model_rhas = '""'.join([str($model.rhas_model), str($model.rhas_cat_count)])
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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29 #else
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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30 #set model_rhas = str($model.rhas_model)
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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31 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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32 --model ${model_matrix}${model.base_freqs}${model_rhas}
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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33 #elif $model.model_type == 'single_string'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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34 --model '${model.model_string}'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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35 #elif $model.model_type == 'multi_file'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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36 --model '$model.model_file'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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37 --brlen $model.brlen_linkage
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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38 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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39 #set start_trees = []
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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40 #if $tree_file:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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41 #set start_trees = start_trees + [str($tree_file)]
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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42 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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43 #if $tree_pars_count:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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44 #set start_trees = start_trees + ['""'.join(["pars{", str($tree_pars_count), "}"])]
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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45 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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46 #if $tree_rand_count:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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47 #set start_trees = start_trees + ['""'.join(["rand{", str($tree_rand_count), "}"])]
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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48 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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49 #set tree_str = '","'.join($start_trees)
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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50 #if $tree_str:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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51 --tree $tree_str
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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52 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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53 #if $outgroup_name:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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54 --outgroup '$outgroup_name'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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55 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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56 #if $constraint_file:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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57 --tree-constraint '$constraint_file'
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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58 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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59 #if $command == '--all' or $command == '--bootstrap':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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60 #if $bs_metric
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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61 --bs-metric $bs_metric
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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62 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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63 #if $bs_mre:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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64 --bs-trees autoMRE{$bs_reps}
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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65 --bs-cutoff $bs_cutoff
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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66 #else
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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67 --bs- trees $bs_reps
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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68 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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69 #elif $command == '--support':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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70 #if $bs_metric
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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71 --bs-metric $bs_metric
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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72 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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73 --bs-trees $bs_trees
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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74 #elif $command == '--bsconverge':
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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75 --bs-cutoff $bs_cutoff
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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76 --bs-trees $bs_trees
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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77 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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78 #if $random_seed:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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79 --seed $random_seed
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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80 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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81 #if $lh_epsilon:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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82 --lh-epsilon $lh_epsilon
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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83 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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84 #if $lh_epsilon_triplet:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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85 --lh-epsilon-triplet $lh_epsilon_triplet
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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86 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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87 #if $blmin:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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88 --blmin $blmin
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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89 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
90 #if $blmax:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
91 --blmax $blmax
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
92 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
93 $pat_comp
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
94 $site_repeats
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
95 $rate_scalers
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
96 #if $force:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
97 --force $force
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
98 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
99 #if $log_level:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
100 --log $log_level
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
101 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
102 #if $site_weights:
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
103 --site-weights $site_weights
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
104 #end if
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
105 --threads auto{\${GALAXY_SLOTS:-8}}
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
106 ]]></command>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
107 <inputs>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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108 <section name="general_opts" expanded="true" title="General options">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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109 <param name="command" type="select" label="Analysis type">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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110 <option value="--check">Check alignment correctness</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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111 <!-- <option value="-parse">Convert alignment to a compressed binary format (RBA)</option> -->
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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112 <option value="--search" selected="true">Tree search (default)</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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113 <option value="--search1">Tree search (FAST)</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
114 <option value="--all">Tree search with branch support values (SLOW)</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
115 <option value="--evaluate">Optimize branches and model parameters on a fixed topology</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
116 <option value="--start">Generate parsimony and/or random starting trees</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
117 <option value="--bootstrap">Bootstrap tree inference (SLOW)</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
118 <option value="--support">Support value mapping from existing set of bootstrap trees</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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119 <option value="--bsconverge">Bootstopping: Test bootstrap convergerge a posteriori</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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120 <option value="--sitelh">Print per-site log-likelihoods</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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121 <option value="--ancestral">Ancestral state reconstruction on a given tree</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
122 <option value="--rfdist">RF: Compute pair-wise Robinson-Foulds distances between trees</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
123 <option value="--consense">Build a consensus tree</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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124 <option value="--terrace">Check whether a tree lies on a phylogenetic terrace</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
125 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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126 <param name="infile" argument="--msa" type="data" format="fasta,phylip" label="Source file with aligned sequences"
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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127 help="At least four aligned genomes are needed for RAxML-NG." />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
128 <conditional name="model">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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129 <param name="model_type" type="select" display="radio" label="Model type">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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130 <option value="single_gui" selected="true">Single model (GUI)</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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131 <option value="single_string">Single model (string)</option>
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iuc
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132 <option value="multi_file">Partitioned model file</option>
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iuc
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diff changeset
133 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
134 <when value="single_gui">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
135 <conditional name="single_model">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
136 <param name="seq_type" type="select" display="radio" label="Sequence type">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
137 <option value="nucleotide" selected="true">Nucleotide</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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138 <option value="aminoacid">Amino Acid</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
139 <option value="binary">Binary</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
140 <option value="multistate">Multistate</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
141 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
142 <when value="nucleotide">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
143 <param name="subst_matrix" type="select" label="Matrix">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
144 <option value="F81">F81</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
145 <option value="GTR" selected="true">GTR</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
146 <option value="HKY">HKY</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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147 <option value="JC">JC</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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148 <option value="K80">K80</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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149 <option value="SYM">SYM</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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150 <option value="TIM1">TIM1</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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151 <option value="TIM2">TIM2</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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152 <option value="TIM3">TIM3</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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153 <option value="TN93">TN93</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
154 <option value="TPM1">TPM1</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
155 <option value="TPM2">TPM2</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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156 <option value="TPM3">TPM3</option>
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iuc
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diff changeset
157 <option value="TVM">TVM</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
158 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
159 </when>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
160 <when value="aminoacid">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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161 <param name="subst_matrix" type="select" label="Matrix">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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162 <option value="BLOSUM62">BLOSUM62</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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163 <option value="CPREV">CPREV</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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164 <option value="DAYHOFF">DAYHOFF</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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165 <option value="DCMUT">DCMUT</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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166 <option value="FLU">FLU</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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167 <option value="PROTGTR">GTR</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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168 <option value="HIVB">HIVB</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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169 <option value="HIVW">HIVW</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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170 <option value="JTT">JTT</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
diff changeset
171 <option value="JTT-DCMUT">JTT-DCMUT</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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172 <option value="LG" selected="true">LG</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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173 <option value="LG4M">LG4M</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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174 <option value="LG4X">LG4X</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
parents:
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175 <option value="MTART">MTART</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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176 <option value="MTMAM">MTMAM</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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177 <option value="MTREV">MTREV</option>
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178 <option value="MTZOA">MTZOA</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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179 <option value="PMB">PMB</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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180 <option value="RTREV">RTREV</option>
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181 <option value="VT">VT</option>
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iuc
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182 <option value="WAG">WAG</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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183 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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184 </when>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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185 <when value="binary">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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186 <param name="subst_matrix" type="select" label="Matrix">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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187 <option value="BIN">BIN</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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188 </param>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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189 </when>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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190 <when value="multistate">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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191 <param name="multi_state_count" type="integer" value="2" label="Number of states" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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192 <param name="subst_matrix" type="select" label="Matrix">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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193 <option value="MK">MULTIx_MK</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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194 <option value="GTR">MULTIx_GTR</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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195 </param>
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196 </when>
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197 </conditional>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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198 <param name="base_freqs" type="select" label="Stationary base frequencies">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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199 <option value="" selected="true">Default</option>
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200 <option value="+FO">ML estimate</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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201 <option value="+F">empirical</option>
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202 <option value="+FE">equal</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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203 </param>
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204 <param name="rhas_model" type="select" label="Rate heterogeneity across sites (RHAS) model">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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205 <option value="">None / default</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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206 <option value="+G" selected="true">GAMMA</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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207 <option value="+I">Inv</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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208 <option value="+I+G">Inv+GAMMA</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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209 <option value="+R">FreeRate</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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210 <option value="+I+R">Inv+FreeRate</option>
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211 </param>
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212 <param name="rhas_cat_count" type="integer" value="" optional="true" label="Number of RHAS categories" help="Typical range: 2..10 (default: 4)"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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213 </when>
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214 <when value="single_string">
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215 <param name="model_string" type="text" value="" optional="false" label="Model definition string" help="Help: https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model" >
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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216 <sanitizer>
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217 <valid initial="string.ascii_letters,string.digits,string.punctuation">
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218 <remove value="';"/>
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219 </valid>
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220 </sanitizer>
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221 </param>
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222 </when>
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223 <when value="multi_file">
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224 <param name="model_file" type="data" format="txt" label="Partitioned model file" help="Help: https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-models" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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225 <param name="brlen_linkage" type="select" display="radio" label="Branch length linkage among partitions">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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226 <option value="linked">Linked identical</option>
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227 <option value="scaled" selected="true">Linked proportional</option>
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228 <option value="unlinked">Unlinked</option>
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229 </param>
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230 </when>
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231 </conditional>
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232 </section>
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233 <section name="tree_opts" expanded="false" title="Tree options">
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234 <param name="tree_file" type="data" format="nhx" optional="true" label="User starting trees (NEWICK file)" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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235 <param name="tree_pars_count" type="integer" value="" optional="true" label="Number of PARSIMONY starting trees" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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236 <param name="tree_rand_count" type="integer" value="" optional="true" label="Number of RANDOM starting trees" />
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237 <param name="outgroup_name" argument="--outgroup" type="text" value="" optional="true" label="Root a tree: Outgroup taxon name(s)" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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238 <param name="constraint_file" argument="--tree-constraint" type="data" format="txt" optional="true" label="Constraint tree" help="Topological constraint in NEWICK format (can be partial)"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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239 <param name="consensus_type" type="select" display="radio" label="Consensus type">
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240 <option value="strict">Strict</option>
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241 <option value="mr" selected="true">Majority Rule (MR)</option>
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242 <option value="mre">Majority Rule Extended (MRE)</option>
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243 </param>
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244 </section>
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245 <section name="bootstrap_opts" expanded="false" title="Bootstrapping options">
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246 <param name="bs_metric" type="select" multiple="true" display="checkboxes" label="Branch support metric">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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247 <option value="fbp" selected="true">Felsenstein bootstrap</option>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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248 <option value="tbe">Transfer bootstrap (TBE)</option>
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249 </param>
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250 <param name="bs_reps" type="integer" value="1000" min="1" max="10000" label="Number of replicates" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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251 <param name="bs_mre" type="boolean" checked="true" label="Use bootstopping (autoMRE convergence test)" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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252 <param name="bs_cutoff" type="float" value="0.03" min="0" max="1" label="Bootstopping cutoff" help="Cutoff threshold for the MRE-based convergence test" />
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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253 <param argument="--bs-trees" type="data" format="nhx" optional="true" label="Existing set of bootstrap trees"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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254 </section>
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255 <section name="safety_opts" expanded="false" title="Safety checks">
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256 <param argument="--force" type="select" multiple="true" display="checkboxes" label="Disable safety checks (use with CAUTION!)">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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257 <option value="perf">Performance-related (e.g. number of threads)</option>
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258 <option value="msa">MSA-related (e.g. duplicate or gap-only sequences) </option>
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259 <option value="model">Model-related (e,g, invalid state frequencies)</option>
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260 </param>
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261 </section>
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262 <section name="advanced_opts" expanded="false" title="Advanced options">
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263 <param name="random_seed" argument="--seed" type="integer" value="1" label="Random seed" />
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264 <param argument="--lh-epsilon" type="float" value="" optional="true" label="Log-likelihood epsilon for tree search and model optimization" help="Default: 0.1"/>
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265 <param argument="--lh-epsilon-triplet" type="float" value="" optional="true" label="Log-likelihood epsilon for branch length triplet optimization" help="Default: 1000"/>
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266 <param argument="--blmin" type="float" value="" optional="true" label="MIN branch length" help="Default: 10^-6"/>
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267 <param argument="--blmax" type="float" value="" optional="true" label="MAX branch length" help="Default: 100"/>
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268 <param name="pat_comp" type="boolean" truevalue="--pat-comp off" falsevalue="" label="Disable alignment pattern compression" help="Default: NO" />
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269 <param name="site_repeats" type="boolean" truevalue="--site-repeats off" falsevalue="" label="Disable site repeats optimization" help="Default: NO" />
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270 <param name="rate_scalers" type="boolean" truevalue="--rate-scalers on" falsevalue="" label="ALWAYS use individual CLV scalers for each rate category" help="Default: use if MSA has >2000 taxa" />
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271 <param name="log_level" argument="--log" type="select" optional="true" label="Log verbosity">
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272 <option value="error">ERROR</option>
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273 <option value="warning">WARNING</option>
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274 <option value="result">RESULT</option>
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275 <option value="info">INFO</option>
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276 <option value="progress">PROGRESS</option>
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277 <option value="verbose">VERBOSE</option>
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278 <option value="debug">DEBUG</option>
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279 </param>
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280 <param argument="--site-weights" type="data" format="txt" optional="true" label="File with custom MSA column weights (positive integers only!)" />
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281 </section>
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282 </inputs>
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283 <outputs>
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284 <data format="txt" name="log" from_work_dir="galaxy.raxml.log" label="${tool.name} on ${on_string}: Log"/>
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285 <!--
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286 <data format="binary" name="rba" from_work_dir="galaxy.raxml.rba" label="${tool.name} on ${on_string}: RAxML Binary Alignment">
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287 <filter>
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288 general_opts['command'] in ["-parse", "-search", "-search1", "-all"]
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289 </filter>
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290 </data>
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291 -->
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292 <data format="nhx" name="bestTree" from_work_dir="galaxy.raxml.bestTree" label="${tool.name} on ${on_string}: Best-scoring ML Tree">
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293 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--evaluate"] </filter>
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294 </data>
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295 <data format="nhx" name="supportTree" from_work_dir="galaxy.raxml.support" label="${tool.name} on ${on_string}: ML Tree with branch support values">
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296 <filter>general_opts['command'] in ["--all", "--support"] </filter>
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297 </data>
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298 <data format="nhx" name="bootstrapTrees" from_work_dir="galaxy.raxml.bootstraps" label="${tool.name} on ${on_string}: Bootstrap trees">
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299 <filter>general_opts['command'] in ["--all", "--bootstrap"] </filter>
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300 </data>
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301 <data format="txt" name="bestModel" from_work_dir="galaxy.raxml.bestModel" label="${tool.name} on ${on_string}: Optimized model parameters">
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302 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--evaluate"]</filter>
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303 </data>
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304 <data format="nhx" name="startTree" from_work_dir="galaxy.raxml.startTree" label="${tool.name} on ${on_string}: Starting trees">
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305 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--start"] </filter>
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306 </data>
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307 <data format="txt" name="siteLH" from_work_dir="galaxy.raxml.siteLH" label="${tool.name} on ${on_string}: Per-site log-likelihoods">
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308 <filter>general_opts['command'] == "--sitelh"</filter>
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309 </data>
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310 <data format="txt" name="rfDistances" from_work_dir="galaxy.raxml.rfDistances" label="${tool.name} on ${on_string}: Pair-wise RF distances">
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311 <filter>general_opts['command'] == "--rfdist"</filter>
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312 </data>
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313 <data format="txt" name="terrace" from_work_dir="galaxy.raxml.terrace" label="${tool.name} on ${on_string}: Terrace">
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314 <filter>general_opts['command'] == "--terrace"</filter>
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315 </data>
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316 <data format="nhx" name="consensusTreeSTRICT" from_work_dir="galaxy.raxml.consensusTreeSTRICT" label="${tool.name} on ${on_string}: Consensus Tree (strict)">
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317 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "strict" </filter>
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318 </data>
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319 <data format="nhx" name="consensusTreeMR" from_work_dir="galaxy.raxml.consensusTreeMR" label="${tool.name} on ${on_string}: Consensus Tree (MR)">
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320 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "mr" </filter>
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321 </data>
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322 <data format="nhx" name="consensusTreeMRE" from_work_dir="galaxy.raxml.consensusTreeMRE" label="${tool.name} on ${on_string}: Consensus Tree (MRE)">
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323 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "mre" </filter>
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324 </data>
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325 <data format="nhx" name="ancestralTree" from_work_dir="galaxy.raxml.ancestralTree" label="${tool.name} on ${on_string}: Ancestral None-labeled Tree">
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326 <filter>general_opts['command'] == "--ancestral" </filter>
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327 </data>
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328 <data format="txt" name="ancestralStates" from_work_dir="galaxy.raxml.ancestralStates" label="${tool.name} on ${on_string}: Ancestral Sequences">
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329 <filter>general_opts['command'] == "--ancestral" </filter>
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330 </data>
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331 <data format="txt" name="ancestralProbs" from_work_dir="galaxy.raxml.ancestralProbs" label="${tool.name} on ${on_string}: Ancestral Marginal Probabilities">
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332 <filter>general_opts['command'] == "--ancestral" </filter>
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333 </data>
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334 </outputs>
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335 <tests>
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336 <test expect_num_outputs="4">
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337 <section name="general_opts">
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338 <param name="command" value="--search"/>
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339 <param name="infile" value="dna.phy"/>
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340 <conditional name="model">
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341 <param name="model_type" value="single_gui"/>
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342 <conditional name="single_model">
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343 <param name="seq_type" value="nucleotide"/>
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344 <param name="subst_matrix" value="HKY"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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345 </conditional>
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346 </conditional>
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347 </section>
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348 <section name="tree_opts">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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349 <param name="tree_pars_count" value="6"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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350 <param name="tree_rand_count" value="4"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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351 </section>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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352 <section name="advanced_opts">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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diff changeset
353 <param name="random_seed" value="1"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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354 </section>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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diff changeset
355 <output name="log">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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356 <assert_contents>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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357 <has_text text="Final LogLikelihood:"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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358 <has_text text="Elapsed time:"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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359 </assert_contents>
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360 </output>
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361 <output name="startTree" file="tree10.raxml.galaxy" ftype="nhx"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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362 <output name="bestModel">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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363 <assert_contents>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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364 <has_n_columns n="2" sep="="/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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365 <has_n_lines n="1"/>
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366 <has_text text="HKY"/>
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367 </assert_contents>
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368 </output>
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369 <output name="bestTree" ftype="nhx">
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370 <assert_contents>
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371 <has_text_matching expression="Frog"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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372 </assert_contents>
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373 </output>
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374 </test>
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375 <test expect_num_outputs="2">
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diff changeset
376 <section name="general_opts">
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377 <param name="command" value="--consense"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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378 <param name="infile" value="dna.phy"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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379 </section>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
iuc
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diff changeset
380 <section name="tree_opts">
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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381 <param name="tree_file" value="tree10.raxml.galaxy"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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382 <param name="consensus_type" value="mr"/>
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383 </section>
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384 <section name="advanced_opts">
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385 <param name="random_seed" value="1"/>
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386 </section>
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387 <output name="log">
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388 <assert_contents>
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389 <has_text text="run mode: Build consensus tree"/>
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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390 <has_text text="Elapsed time:"/>
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391 </assert_contents>
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392 </output>
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393 <output name="consensusTreeMR" ftype="nhx">
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394 <assert_contents>
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395 <has_text text="Cow"/>
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396 <has_text text="Frog"/>
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397 <has_n_lines n="1"/>
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398 </assert_contents>
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399 </output>
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400 </test>
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401 </tests>
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402 <help><![CDATA[
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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403 RAxML-NG is a phylogenetic tree inference tool which uses Maximum-Likelihood (ML) optimality criterion.
21da84148596 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
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404 Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves,
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405 which allows to quickly navigate to the best-known ML tree.
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406 RAxML-NG is a successor of RAxML 8.x (Stamatakis 2014).
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407
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408 Documentation: https://github.com/amkozlov/raxml-ng/wiki
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409
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410 .. _RAxML-NG: http://www.exelixis-lab.org/web/software/raxml-ng/
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411
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412 ]]></help>
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413 <citations>
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414 <citation type="doi">10.1093/bioinformatics/btz305</citation>
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415 </citations>
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416 </tool>