Mercurial > repos > iuc > fasttree

annotate fasttree.xml @ 3:3aa7c6da1696 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
author iuc
date Sat, 05 Oct 2024 10:02:39 +0000
parents e005e659ae21
children bc939965ce41
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3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
iuc
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1 <tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy3" profile="23.1">
2
e005e659ae21 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 3b044152a60cd46b50ab58bc15af2d9a9cf2c86d"
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2 <description>build maximum-likelihood phylogenetic trees</description>
0
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3 <macros>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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4 <token name="@VERSION@">2.1.10</token>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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5 </macros>
3
3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
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6 <xrefs>
3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
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7 <xref type="bio.tools">fasttree</xref>
3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
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8 </xrefs>
0
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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9 <requirements>
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ef46a404db96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 7cef8f26706035207d601ba0f0a37edbb2be9664"
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10 <requirement type="package" version="@VERSION@">fasttree</requirement>
0
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11 </requirements>
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3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
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12 <version_command><![CDATA[FastTree 2>&1 >/dev/null | head -n 1 | cut -d" " -f 5]]></version_command>
0
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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13 <command detect_errors="aggressive">
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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14 <![CDATA[
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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15 FastTree
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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16
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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17 $model_selector.format
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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18 $model_selector.model
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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19 -nopr
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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20 #if $input_selector.select_format == 'fasta':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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21 $input_selector.quote
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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22 #else if $input_selector.select_format == 'phylip':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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23 -n $input_selector.num
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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24 #end if
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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25 #set $inform = $input_selector.intree_selector.intree_format
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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26 #if $inform == 'one':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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27 -intree1 '$input_selector.intree_selector.start_tree'
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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28 #else if $inform == 'many':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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29 -intree '$input_selector.intree_selector.start_tree'
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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30 #end if
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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31 #if $advanced_selector.maximize == 'max':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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32 #if $advanced_selector.cat_selector.conrate == 'no':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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33 -cat $advanced_selector.cat_selector.ratecat
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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34 #else if $advanced_selector.cat_selector.conrate == 'yes':
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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35 -nocat
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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36 #end if
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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37 $advanced_selector.gamma
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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38 $advanced_selector.nosupport
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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39 $advanced_selector.mllen
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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40 $advanced_selector.likelihood
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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41 $advanced_selector.fastest
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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42 $advanced_selector.pseudo
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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43 #end if
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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44
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45 < '$input' > '$output'
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46
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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47 #if $save_logfile:
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48 2> '$log'
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49 #end if
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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50 ]]>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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51 </command>
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52 <inputs>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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53 <conditional name="input_selector">
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54 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)">
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55 <option value="fasta" selected="true">fasta</option>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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56 <option value="phylip">phylip</option>
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57 </param>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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58 <when value="fasta">
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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59 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/>
3
3aa7c6da1696 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
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60 <param argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." />
0
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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61 <conditional name="intree_selector">
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62 <param name="intree_format" type="select" label="Set starting tree(s)">
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63 <option value="none" selected="true">No starting trees</option>
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64 <option value="one">Use starting tree</option>
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65 </param>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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66 <when value="none">
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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67 </when>
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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68 <when value="one">
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69 <param format="nhx" name="start_tree" type="data" label="Newick file" />
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70 </when>
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71 </conditional>
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72 </when>
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73 <when value="phylip">
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74 <param format="phylip" name="input" type="data" label="PHYLIP file" />
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75 <param name="num" type="integer" value="1" optional="true" label="Number of multiple alignments" />
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76 <conditional name="intree_selector">
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77 <param name="intree_format" type="select" label="Set starting tree(s)">
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78 <option value="none" selected="true">No starting trees</option>
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79 <option value="one">One tree for multiple alignments</option>
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80 <option value="many">Multiple trees for multiple alignments</option>
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81 </param>
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82 <when value="none">
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83 </when>
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84 <when value="one">
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85 <param format="nhx" name="start_tree" type="data" multiple="false" label="Newick file" />
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86 </when>
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87 <when value="many">
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88 <param format="nhx" name="start_tree" type="data" label="Newick file" multiple="false" help="The tree produced by the full alignment to be used as a starting point for each bootstrapping replicate. This will save considerable computation time." />
c7e73acfa3eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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89 </when>
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90 </conditional>
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91 </when>
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92 </conditional>
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93 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" checked="false" label="Save log file output" />
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94 <conditional name="model_selector">
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95 <param name="format" type="select" label="Protein or nucleotide alignment" help="Specify if the aligned sequences are nucleotide or protein sequences">
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96 <option value="-nt">Nucleotide</option>
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97 <option value="" selected="true">Protein</option>
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98 </param>
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99 <when value="-nt">
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100 <param name="model" type="select" label="Nucleotide evolution model">
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101 <option value="-gtr" selected="true">GTR+CAT</option>
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102 <option value="">Jukes-Cantor + CAT</option>
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103 </param>
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104 </when>
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105 <when value="">
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106 <param name="model" type="select" label="Protein evolution model">
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107 <option value="" selected="true">JTT + CAT</option>
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108 <option value="-wag">WAG + CAT</option>
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109 <option value="-lg">LG + CAT</option>
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110 </param>
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111 </when>
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112 </conditional>
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113 <conditional name="advanced_selector">
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114 <param name="maximize" type="select" label="Show advanced options">
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115 <option value="min" selected="true">No</option>
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116 <option value="max">Yes</option>
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117 </param>
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118 <when value="min">
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119 </when>
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120 <when value="max">
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121 <conditional name="cat_selector">
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122 <param name="conrate" type="select" label="Use constant rates?">
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123 <option value="no" selected="true">Do not use constant rates.</option>
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124 <option value="yes">Use constant rates.</option>
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125 </param>
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126 <when value="no">
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127 <param name="ratecat" type="integer" value="20" label="Specify the number of rate categories of sites (default 20)" />
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128 </when>
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129 <when value="yes">
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130 </when>
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131 </conditional>
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132 <param value="gamma" argument="-gamma" type="boolean" truevalue="-gamma" falsevalue="" checked="false" label="Use Gamma20" help="After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood." />
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133 <param value="nosupport" argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue="" checked="false" label="Eliminates the support value computation. Support value computation is not recommended for wide alignments."/>
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134 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." />
3
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135 <param argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" />
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136 <param argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." />
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137 <param argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." />
0
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138 </when>
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139 </conditional>
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140 </inputs>
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141 <outputs>
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142 <data name="output" format="nhx" label="${tool.name} on ${on_string}:tree.nhx" />
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143 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt">
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144 <filter>save_logfile</filter>
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145 </data>
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146 </outputs>
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147 <tests>
3
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148 <test expect_num_outputs="2">
0
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149 <param name="select_format" value="fasta" />
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150 <param name="model" value="" />
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151 <param name="input" value="aligned.fasta" />
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152 <param name="format" value="-nt" />
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153 <param name="save_logfile" value="true" />
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154 <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" />
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155 <output name="log" file="log.txt" ftype="txt" compare="contains" />
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156 </test>
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157 </tests>
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158 <help>
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159 <![CDATA[
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160
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161 ===========
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162 Description
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163 ===========
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164
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165 .. class:: infomark
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166
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167 FastTree_ infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software.
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168
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169 .. _FastTree: http://meta.microbesonline.org/fasttree
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170
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171 -----
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172
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173 -----
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174 Input
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175 -----
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176
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177 A) Aligned sequences file in FASTA format (e.g. the alignment from the 'PyNAST' tool) or PHYLIP format.
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178 B) Newick file to set the starting tree(s) (optional)
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179
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180 ----------
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181 Parameters
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182 ----------
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183
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184 Nucleotide or protein alignment
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185 To specify the type of sequence alignment (nucleotide or protein) you are providing.
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186
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187 Nucleotide evolution model
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188 Specify GTR+CAT (Generalized Time Reversable Model) or Jukes-Cantor + CAT.
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189
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190 Protein evolution model
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191 Specify JTT (Jones-Taylor-Thornton 1992 model) + CAT, WAG (Whelan-And-Goldman 2001 model) + CAT, or LG (Le-Gascuel 2008 model) + CAT.
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192
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193 Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree. (fasta only)
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194 FastTree will not be able to read these trees back in. (-quote)
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195
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196 Number of multiple alignments (phylip only)
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197 (-n)
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198
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199 -------------------
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200 Advanced Parameters
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201 -------------------
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202
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203 Number of rates of sites
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204 Defaults to 20. Specify whether you wish to choose constant rates. (-cat/-nocat)
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205
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206 Use Gamma20
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207 After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood. (-gamma)
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208
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209 Eliminates the support value computation. Support value computation is not recommended for wide alignments.
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210 (-nosupport)
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211
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212 Turn off maximum-likelihood.
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213 (-noml)
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214
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215 Speed up the neighbor joining phase and reduce memory usage
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216 Recommended for >50,000 sequences. (-fastest)
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217
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218 Use pseudocounts
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219 Recommended if you have many fragmentary sequences. (-pseudo)
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220
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221 Optimize branch lengths without ML NNIs.
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222 (-mllen)
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223
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224 ------
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225 Output
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226 ------
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227
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228 This tool produces two output files, one of which is optional (the log file).
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229
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230 (A) The phylogenetic tree in Newick_ format (nhx).
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231
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232 (B) *(optional)* The log file, containing information of the FastTree run to build the phylogenetic tree.
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233
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234 .. class:: infomark
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235
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236 The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences.
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237
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238 .. _Newick: http://en.wikipedia.org/wiki/Newick_format
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239
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240 -----
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241
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242
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243 =========
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244 Resources
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245 =========
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246
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247 FastTree_v2.1.10_
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248
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249 .. _FastTree_v2.1.10: http://meta.microbesonline.org/fasttree/#Install
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250 ]]>
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251 </help>
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252 <citations>
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253 <citation type="doi">10.1371/journal.pone.0009490</citation>
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254 </citations>
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255 </tool>