Mercurial > repos > iuc > fasttree

annotate fasttree.xml @ 5:e368780552ad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit a90964e5fc45313b74753e1686575102475825b0
author iuc
date Mon, 16 Dec 2024 13:33:45 +0000
parents 66e48435be9a
children
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66e48435be9a 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
6c9eef7ca7ef "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>
4
66e48435be9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
iuc
parents: 3
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3 <macros>
66e48435be9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
iuc
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4 <token name="@VERSION@">2.1.10</token>
66e48435be9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
iuc
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5 </macros>
3
70f85ee4f242 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <xrefs>
70f85ee4f242 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <xref type="bio.tools">fasttree</xref>
70f85ee4f242 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 </xrefs>
0
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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9 <requirements>
1
72ad35752216 "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
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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11 </requirements>
3
70f85ee4f242 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 <version_command><![CDATA[FastTree 2>&1 >/dev/null | head -n 1 | cut -d" " -f 5]]></version_command>
0
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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13 <command detect_errors="aggressive">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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14 <![CDATA[
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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15 FastTree
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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16
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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17 $model_selector.format
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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18 $model_selector.model
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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19 -nopr
a415bf349f95 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':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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21 $input_selector.quote
a415bf349f95 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':
a415bf349f95 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
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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24 #end if
a415bf349f95 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
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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26 #if $inform == 'one':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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27 -intree1 '$input_selector.intree_selector.start_tree'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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28 #else if $inform == 'many':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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29 -intree '$input_selector.intree_selector.start_tree'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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30 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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31 #if $advanced_selector.maximize == 'max':
a415bf349f95 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':
a415bf349f95 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
a415bf349f95 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':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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35 -nocat
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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36 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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37 $advanced_selector.gamma
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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38 $advanced_selector.nosupport
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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39 $advanced_selector.mllen
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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40 $advanced_selector.likelihood
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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41 $advanced_selector.fastest
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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42 $advanced_selector.pseudo
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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43 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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44
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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45 < '$input' > '$output'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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46
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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47 #if $save_logfile:
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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48 2> '$log'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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49 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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50 ]]>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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51 </command>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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52 <inputs>
a415bf349f95 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">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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54 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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55 <option value="fasta" selected="true">fasta</option>
a415bf349f95 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>
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58 <when value="fasta">
a415bf349f95 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"/>
4
66e48435be9a 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
a415bf349f95 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">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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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>
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66 <when value="none">
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67 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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68 <when value="one">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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69 <param format="nhx" name="start_tree" type="data" label="Newick file" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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70 </when>
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71 </conditional>
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72 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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73 <when value="phylip">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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74 <param format="phylip" name="input" type="data" label="PHYLIP file" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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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">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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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." />
a415bf349f95 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>
5
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93 <param name="save_logfile" type="boolean" checked="false" label="Save log file output" />
0
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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">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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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">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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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." />
4
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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>
4
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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>
5
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157 <test expect_num_outputs="1">
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158 <param name="select_format" value="fasta" />
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159 <param name="model" value="" />
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160 <param name="input" value="aligned.fasta" />
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161 <param name="format" value="-nt" />
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162 <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" />
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163 </test>
0
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164 </tests>
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165 <help>
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166 <![CDATA[
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167
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168 ===========
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169 Description
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170 ===========
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171
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172 .. class:: infomark
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173
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174 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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175
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176 .. _FastTree: http://meta.microbesonline.org/fasttree
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177
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178 -----
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179
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180 -----
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181 Input
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182 -----
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183
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184 A) Aligned sequences file in FASTA format (e.g. the alignment from the 'PyNAST' tool) or PHYLIP format.
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185 B) Newick file to set the starting tree(s) (optional)
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186
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187 ----------
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188 Parameters
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189 ----------
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190
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191 Nucleotide or protein alignment
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192 To specify the type of sequence alignment (nucleotide or protein) you are providing.
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193
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194 Nucleotide evolution model
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195 Specify GTR+CAT (Generalized Time Reversable Model) or Jukes-Cantor + CAT.
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196
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197 Protein evolution model
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198 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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199
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200 Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree. (fasta only)
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201 FastTree will not be able to read these trees back in. (-quote)
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202
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203 Number of multiple alignments (phylip only)
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204 (-n)
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205
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206 -------------------
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207 Advanced Parameters
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208 -------------------
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209
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210 Number of rates of sites
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211 Defaults to 20. Specify whether you wish to choose constant rates. (-cat/-nocat)
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212
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213 Use Gamma20
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214 After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood. (-gamma)
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215
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216 Eliminates the support value computation. Support value computation is not recommended for wide alignments.
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217 (-nosupport)
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218
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219 Turn off maximum-likelihood.
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220 (-noml)
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221
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222 Speed up the neighbor joining phase and reduce memory usage
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223 Recommended for >50,000 sequences. (-fastest)
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224
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225 Use pseudocounts
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226 Recommended if you have many fragmentary sequences. (-pseudo)
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227
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228 Optimize branch lengths without ML NNIs.
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229 (-mllen)
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230
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231 ------
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232 Output
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233 ------
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234
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235 This tool produces two output files, one of which is optional (the log file).
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236
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237 (A) The phylogenetic tree in Newick_ format (nhx).
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238
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239 (B) *(optional)* The log file, containing information of the FastTree run to build the phylogenetic tree.
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240
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241 .. class:: infomark
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242
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243 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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244
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245 .. _Newick: http://en.wikipedia.org/wiki/Newick_format
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246
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247 -----
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248
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249
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250 =========
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251 Resources
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252 =========
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253
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254 FastTree_v2.1.10_
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255
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256 .. _FastTree_v2.1.10: http://meta.microbesonline.org/fasttree/#Install
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257 ]]>
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258 </help>
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259 <citations>
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260 <citation type="doi">10.1371/journal.pone.0009490</citation>
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261 </citations>
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262 </tool>