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annotate ete_mod.xml @ 3:077021c45b96 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
author earlhaminst
date Mon, 12 Mar 2018 12:51:48 -0400
parents 03c10736e497
children d40b9a7debe5
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2
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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1 <tool id="ete3_mod" name="ETE mod" version="@VERSION@">
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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2 <description>manipulates tree topology by rooting, pruning or sorting branches</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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8 ete3 mod -t
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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9 #for $input_tree in $input_trees:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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10 '$input_tree'
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11 #end for
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12 -v '$verbosity'
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13 #if $outgroup:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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14 --outgroup '$outgroup'
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15 #end if
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16 ## #if float($ultrametric) > 0.0:
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17 ## --ultrametric $ultrametric
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18 ## #end if
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19 #if $prune:
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20 #set node_list = "'" + "' '".join($prune.split(',')) + "'"
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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21 --prune $node_list
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22 #end if
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23 $prune_preserve_lengths
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24 $unroot
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25 $sort_branches
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26 $ladderize
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27 $resolve_polytomies
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28 $standardize
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29 > '$output_tree'
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30 ]]></command>
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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31 <inputs>
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32 <param name="input_trees" argument="-t" type="data" format="nhx" multiple="true" label="Newick trees" />
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33 <param name="verbosity" argument="-v" type="integer" value="0" min="0" max="4" label="Verbosity level"
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34 help="0=totally quite, 1=errors only, 2=warning+errors, 3=info+warnings+errors 4=debug (-v)" />
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35 <param argument="--outgroup" type="text" value="" label="Reroot tree with outgroup (space separated list of leaf names)"
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36 help="Root the tree using the provided outgroup. If several
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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37 names are provided, the first common ancestor grouping
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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38 all of them will be selected as outgroup" />
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39 <!-- parameter does not work in the current version
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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40 <param argument="- -ultrametric" type="float" value="0" min="0" label="Convert tree into ultrametric"
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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41 help="Convert tree into ultrametric (all leaves have the
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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42 same distance to root). If an argument (!=0) is provided, it
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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43 will be used as the expected tree length" />-->
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44 <param argument="--prune" type="text" value="" label="Prune nodes from the tree (comma-separated list of leaf names)"
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45 help="Remove all nodes in the tree except the ones provided (empty does not prune)" />
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46 <param argument="--prune_preserve_lengths" type="boolean" truevalue="--prune_preserve_lengths" falsevalue="" label="Prune: preserve length"
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47 help="Branch lengths of the removed nodes are added to the kept branches, thus preserving original tree length" />
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48 <param argument="--unroot" type="boolean" truevalue="--unroot" falsevalue="" label="Unroots the tree" />
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49 <param argument="--sort_branches" type="boolean" truevalue="--sort_branches" falsevalue="" label="Sort branches"
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50 help="Sort branches according to node names" />
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51 <param argument="--ladderize" type="boolean" truevalue="--ladderize" falsevalue="" label="Ladderize"
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52 help="Sort branches by partition size" />
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53 <param argument="--resolve_polytomies" type="boolean" truevalue="--resolve_polytomies" falsevalue="" label="Resolve polytomies"
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54 help="Converts polytomies into bifurcations" />
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55 <param argument="--standardize" type="boolean" truevalue="--standardize" falsevalue="" label="Standardize tree"
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56 help="Standardize tree topology by expanding polytomies and single child nodes" />
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57 </inputs>
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58 <outputs>
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59 <data name="output_tree" format="nhx" label="${tool.name} on ${on_string}"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
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64 <param name="outgroup" value="A" />
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65 <output name="output_tree" file="tree1_ogA.nhx" />
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66 </test>
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67 <test>
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68 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
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69 <param name="prune" value="A,C" />
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70 <output name="output_tree" file="tree1_pruneAC.nhx" />
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71 </test>
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72 <test>
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73 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
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74 <param name="prune" value="A,C" />
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75 <param name="prune_preserve_lengths" value="--prune_preserve_lengths" />
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76 <output name="output_tree" file="tree1_pruneACpreserve.nhx" />
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77 </test>
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78 <test>
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79 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
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80 <param name="unroot" value="--unroot" />
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81 <output name="output_tree" file="tree1_unroot.nhx" />
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82 </test>
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83 <test>
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84 <param name="input_trees" ftype="nhx" value="tree2.nhx" />
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85 <param name="sort_branches" value="--sort_branches" />
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86 <output name="output_tree" file="tree2_sort.nhx" />
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87 </test>
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88 <test>
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89 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
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90 <param name="ladderize" value="--ladderize" />
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91 <output name="output_tree" file="tree1_ladder.nhx" />
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92 </test>
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93 <test>
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94 <param name="input_trees" ftype="nhx" value="tree1_unroot.nhx" />
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95 <param name="resolve_polytomies" value="--resolve_polytomies" />
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96 <output name="output_tree" file="tree1_unroot_resolve.nhx" />
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97 </test>
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98 <test>
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99 <param name="input_trees" ftype="nhx" value="tree3.nhx" />
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100 <param name="standardize" value="--standardize" />
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101 <output name="output_tree" file="tree3_stand.nhx" />
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102 </test>
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103 </tests>
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104 <help><![CDATA[
3
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105 Modify a given input tree using the `ETE Toolkit`_.
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106
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107 .. _ETE Toolkit: http://etetoolkit.org/
2
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108 ]]></help>
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109 <expand macro="citations" />
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110 </tool>