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comparison ete_genetree_splitter.xml @ 16:e4d5d9a69c9d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:28:17 +0000
parents 1e85af7a29c4
children
comparison
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15:1e85af7a29c4 16:e4d5d9a69c9d
1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@"> 1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>from a genetree using the ETE Toolkit</description> 2 <description>from a genetree using the ETE Toolkit</description>
3 <macros> 3 <macros>
4 <import>ete_macros.xml</import> 4 <import>ete_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
89 </outputs> 89 </outputs>
90 <tests> 90 <tests>
91 <test> 91 <test>
92 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 92 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
93 <param name="gene_node" value="0"/> 93 <param name="gene_node" value="0"/>
94 <param name="splitter" value="dups"/> 94 <conditional name="splitting_conditional">
95 <param name="splitter" value="dups"/>
96 </conditional>
95 <param name="output_format" value="9" /> 97 <param name="output_format" value="9" />
96 <output_collection name="genetrees_lists" type="list" count="4"> 98 <output_collection name="genetrees_lists" type="list" count="4">
97 <element name="1" file="11_genetree.nhx" ftype="nhx" /> 99 <element name="1" file="11_genetree.nhx" ftype="nhx" />
98 <element name="2" file="12_genetree.nhx" ftype="nhx" /> 100 <element name="2" file="12_genetree.nhx" ftype="nhx" />
99 <element name="3" file="13_genetree.nhx" ftype="nhx" /> 101 <element name="3" file="13_genetree.nhx" ftype="nhx" />
101 </output_collection> 103 </output_collection>
102 </test> 104 </test>
103 <test> 105 <test>
104 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 106 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
105 <param name="gene_node" value="0"/> 107 <param name="gene_node" value="0"/>
106 <param name="splitter" value="dups"/> 108 <conditional name="splitting_conditional">
107 <param name="gainlose" value="True" /> 109 <param name="splitter" value="dups"/>
108 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" /> 110 </conditional>
109 <param name="species_format" value="8" /> 111 <conditional name="gainlose_conditional">
112 <param name="gainlose" value="True" />
113 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
114 <param name="species_format" value="8" />
115 </conditional>
110 <param name="output_format" value="9" /> 116 <param name="output_format" value="9" />
111 <output_collection name="genetrees_lists" type="list" count="5"> 117 <output_collection name="genetrees_lists" type="list" count="5">
112 <element name="1" file="21_genetree.nhx" ftype="nhx" /> 118 <element name="1" file="21_genetree.nhx" ftype="nhx" />
113 <element name="2" file="22_genetree.nhx" ftype="nhx" /> 119 <element name="2" file="22_genetree.nhx" ftype="nhx" />
114 <element name="3" file="23_genetree.nhx" ftype="nhx" /> 120 <element name="3" file="23_genetree.nhx" ftype="nhx" />
117 </output_collection> 123 </output_collection>
118 </test> 124 </test>
119 <test> 125 <test>
120 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 126 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
121 <param name="gene_node" value="0"/> 127 <param name="gene_node" value="0"/>
122 <param name="splitter" value="treeko"/> 128 <conditional name="splitting_conditional">
129 <param name="splitter" value="treeko"/>
130 </conditional>
123 <param name="output_format" value="9" /> 131 <param name="output_format" value="9" />
124 <output_collection name="genetrees_lists" type="list" count="4"> 132 <output_collection name="genetrees_lists" type="list" count="4">
125 <element name="1" file="31_genetree.nhx" ftype="nhx" /> 133 <element name="1" file="31_genetree.nhx" ftype="nhx" />
126 <element name="2" file="32_genetree.nhx" ftype="nhx" /> 134 <element name="2" file="32_genetree.nhx" ftype="nhx" />
127 <element name="3" file="33_genetree.nhx" ftype="nhx" /> 135 <element name="3" file="33_genetree.nhx" ftype="nhx" />
130 </test> 138 </test>
131 139
132 <test> 140 <test>
133 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 141 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
134 <param name="gene_node" value="0"/> 142 <param name="gene_node" value="0"/>
135 <param name="splitter" value="species"/> 143 <conditional name="splitting_conditional">
136 <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" /> 144 <param name="splitter" value="species"/>
137 <param name="outgroup" value="susscrofa" /> 145 <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
146 <param name="outgroup" value="susscrofa" />
147 </conditional>
138 <param name="output_format" value="9" /> 148 <param name="output_format" value="9" />
139 <output_collection name="genetrees_lists" type="list" count="4"> 149 <output_collection name="genetrees_lists" type="list" count="4">
140 <element name="1" file="41_genetree.nhx" ftype="nhx" /> 150 <element name="1" file="41_genetree.nhx" ftype="nhx" />
141 <element name="2" file="42_genetree.nhx" ftype="nhx" /> 151 <element name="2" file="42_genetree.nhx" ftype="nhx" />
142 <element name="3" file="43_genetree.nhx" ftype="nhx" /> 152 <element name="3" file="43_genetree.nhx" ftype="nhx" />