Mercurial > repos > earlhaminst > ete

annotate ete_genetree_splitter.xml @ 14:d40b9a7debe5 draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 71b9c1035f713be174bfcf5ecb20804495f39258
author earlhaminst
date Thu, 07 Mar 2024 19:39:30 +0000
parents dc32007a6b36
children
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dc32007a6b36 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
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1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@+galaxy1">
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2 <description>from a genetree using the ETE Toolkit</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
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5 </macros>
14
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <stdio>
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9 <!-- Anything other than zero is an error -->
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10 <exit_code range="1:" />
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11 </stdio>
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12 <command><![CDATA[
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13 python '$__tool_directory__/ete_genetree_splitter.py'
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14 --genetree '$genetreeFile'
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15 --gene_node $gene_node
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16 --split $splitting_conditional.splitter
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17 #if $gainlose_conditional.gainlose == "True"
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18 --speciestree '$gainlose_conditional.speciesFile'
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19 --species_format $gainlose_conditional.species_format
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20 --gainlose
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21 #end if
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22 #if $splitting_conditional.splitter == "species"
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23 --ingroup '$splitting_conditional.ingroup'
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24 --outgroup '$splitting_conditional.outgroup'
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25 #end if
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26 --output_format $output_format
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27 ]]></command>
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28 <inputs>
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29 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" />
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30 <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option">
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31 <option value="0" selected="true">gene_species</option>
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32 <option value="1">species_gene</option>
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33 </param>
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34 <conditional name="splitting_conditional">
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35 <param name="splitter" type="select" label="GeneTree splitting algorithm">
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36 <option value="dups">Split by Duplication</option>
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37 <option value="treeko">Split using TreeKO algorithm</option>
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38 <option value="species">Split using In-group and Out-group species</option>
dc32007a6b36 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
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39 </param>
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40 <when value="dups" />
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41 <when value="treeko" />
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42 <when value="species">
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43 <param name="ingroup" type="text" label="In-group species list" help="Comma-separated species list without whitespaces or special characters" />
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44 <param name="outgroup" type="text" label="Out-group species list" help="Comma-separated species list without whitespaces or special characters" />
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45 </when>
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46 </conditional>
3
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47 <conditional name="gainlose_conditional">
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48 <param name="gainlose" type="select" label="Find out gene gain/lose">
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49 <option value="True">Yes</option>
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50 <option value="False" selected="true">No</option>
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51 </param>
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52 <when value="False" />
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53 <when value="True">
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54 <param name="speciesFile" type="data" format="nhx" label="Species file" help="Species Tree in nhx format" />
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55 <param name="species_format" type="select" label="Input species tree format" help="See table below">
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56 <option value="0">Flexible with support values (0)</option>
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57 <option value="1">Flexible with internal node names (1)</option>
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58 <option value="2">All branches + leaf names + internal supports (2)</option>
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59 <option value="3">All branches + all names (3)</option>
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60 <option value="4">Leaf branches + leaf names (4)</option>
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61 <option value="5">Internal and leaf branches + leaf names (5)</option>
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62 <option value="6">Internal branches + leaf names (6)</option>
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63 <option value="7">Leaf branches + all names (7)</option>
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64 <option value="8" selected="true">All names (8)</option>
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65 <option value="9">Leaf names (9)</option>
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66 <option value="100">Topology only (100)</option>
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67 </param>
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68 </when>
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69 </conditional>
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70
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71 <param name="output_format" type="select" label="Output GeneTree format" help="See table below">
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72 <option value="0">Flexible with support values (0)</option>
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73 <option value="1">Flexible with internal node names (1)</option>
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74 <option value="2">All branches + leaf names + internal supports (2)</option>
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75 <option value="3">All branches + all names (3)</option>
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76 <option value="4">Leaf branches + leaf names (4)</option>
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77 <option value="5">Internal and leaf branches + leaf names (5)</option>
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78 <option value="6">Internal branches + leaf names (6)</option>
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79 <option value="7">Leaf branches + all names (7)</option>
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80 <option value="8">All names (8)</option>
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81 <option value="9" selected="true">Leaf names (9)</option>
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82 <option value="100">Topology only (100)</option>
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83 </param>
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84 </inputs>
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85 <outputs>
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86 <collection name="genetrees_lists" type="list" label="${tool.name} on ${on_string}">
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earlhaminst
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87 <discover_datasets pattern="(?P&lt;designation&gt;.+)_genetree\.nhx" ext="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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88 </collection>
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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93 <param name="gene_node" value="0"/>
9
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94 <param name="splitter" value="dups"/>
3
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earlhaminst
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95 <param name="output_format" value="9" />
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96 <output_collection name="genetrees_lists" type="list" count="4">
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97 <element name="1" file="11_genetree.nhx" ftype="nhx" />
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98 <element name="2" file="12_genetree.nhx" ftype="nhx" />
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99 <element name="3" file="13_genetree.nhx" ftype="nhx" />
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100 <element name="4" file="14_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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101 </output_collection>
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102 </test>
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103 <test>
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104 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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105 <param name="gene_node" value="0"/>
9
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106 <param name="splitter" value="dups"/>
3
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107 <param name="gainlose" value="True" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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108 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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109 <param name="species_format" value="8" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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110 <param name="output_format" value="9" />
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111 <output_collection name="genetrees_lists" type="list" count="5">
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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112 <element name="1" file="21_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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113 <element name="2" file="22_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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114 <element name="3" file="23_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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115 <element name="4" file="24_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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116 <element name="5" file="25_genetree.nhx" ftype="nhx" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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117 </output_collection>
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118 </test>
9
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119 <test>
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120 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
b29ee6a16524 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
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121 <param name="gene_node" value="0"/>
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122 <param name="splitter" value="treeko"/>
b29ee6a16524 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
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123 <param name="output_format" value="9" />
12
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124 <output_collection name="genetrees_lists" type="list" count="4">
9
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125 <element name="1" file="31_genetree.nhx" ftype="nhx" />
b29ee6a16524 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
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126 <element name="2" file="32_genetree.nhx" ftype="nhx" />
b29ee6a16524 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
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127 <element name="3" file="33_genetree.nhx" ftype="nhx" />
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128 <element name="4" file="34_genetree.nhx" ftype="nhx" />
b29ee6a16524 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
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129 </output_collection>
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130 </test>
12
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131
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132 <test>
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133 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
dc32007a6b36 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
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134 <param name="gene_node" value="0"/>
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135 <param name="splitter" value="species"/>
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136 <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
dc32007a6b36 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
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137 <param name="outgroup" value="susscrofa" />
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138 <param name="output_format" value="9" />
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139 <output_collection name="genetrees_lists" type="list" count="4">
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140 <element name="1" file="41_genetree.nhx" ftype="nhx" />
dc32007a6b36 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
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141 <element name="2" file="42_genetree.nhx" ftype="nhx" />
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142 <element name="3" file="43_genetree.nhx" ftype="nhx" />
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143 <element name="4" file="44_genetree.nhx" ftype="nhx" />
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144 </output_collection>
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145 </test>
3
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146 </tests>
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147 <help><![CDATA[
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148 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.
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149
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150 .. _ETE Toolkit: http://etetoolkit.org/
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151
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152 **Output format:**
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153
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154 ======= ============================================= ========================================================================================
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155 FORMAT DESCRIPTION SAMPLE
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156 ------- --------------------------------------------- ----------------------------------------------------------------------------------------
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157 0 flexible with support values ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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158 1 flexible with internal node names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
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159 2 all branches + leaf names + internal supports ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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160 3 all branches + all names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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161 4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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162 5 internal and leaf branches + leaf names ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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163 6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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164 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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165 8 all names ((D,F)E,(B,H)B);
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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166 9 leaf names ((D,F),(B,H));
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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167 100 topology only ((,),(,));
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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168 ======= ============================================= ========================================================================================
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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169 ]]></help>
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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170 <expand macro="citations" />
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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171 </tool>