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comparison ete_genetree_splitter.xml @ 9:b29ee6a16524 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
author earlhaminst
date Tue, 20 Oct 2020 15:10:40 +0000
parents f1eca1158f21
children 541a2ffc01ff
comparison
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8:16e925bf567e 9:b29ee6a16524
1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@"> 1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@+galaxy1">
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="requirements" /> 6 <expand macro="requirements" />
10 </stdio> 10 </stdio>
11 <command><![CDATA[ 11 <command><![CDATA[
12 python '$__tool_directory__/ete_genetree_splitter.py' 12 python '$__tool_directory__/ete_genetree_splitter.py'
13 --genetree '$genetreeFile' 13 --genetree '$genetreeFile'
14 --gene_node $gene_node 14 --gene_node $gene_node
15 --split $splitter
15 #if $gainlose_conditional.gainlose == "True" 16 #if $gainlose_conditional.gainlose == "True"
16 --speciestree '$gainlose_conditional.speciesFile' 17 --speciestree '$gainlose_conditional.speciesFile'
17 --species_format $gainlose_conditional.species_format 18 --species_format $gainlose_conditional.species_format
18 --gainlose 19 --gainlose
19 #end if 20 #end if
22 <inputs> 23 <inputs>
23 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" /> 24 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" />
24 <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option"> 25 <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option">
25 <option value="0" selected="true">gene_species</option> 26 <option value="0" selected="true">gene_species</option>
26 <option value="1">species_gene</option> 27 <option value="1">species_gene</option>
28 </param>
29 <param name="splitter" type="select" label="GeneTree splitting algorithm">
30 <option value="dups">Split by Duplication</option>
31 <option value="treeko">Split using TreeKO algorithm</option>
27 </param> 32 </param>
28 <conditional name="gainlose_conditional"> 33 <conditional name="gainlose_conditional">
29 <param name="gainlose" type="select" label="Find out gene gain/lose"> 34 <param name="gainlose" type="select" label="Find out gene gain/lose">
30 <option value="True">Yes</option> 35 <option value="True">Yes</option>
31 <option value="False" selected="true">No</option> 36 <option value="False" selected="true">No</option>
70 </outputs> 75 </outputs>
71 <tests> 76 <tests>
72 <test> 77 <test>
73 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 78 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
74 <param name="gene_node" value="0"/> 79 <param name="gene_node" value="0"/>
80 <param name="splitter" value="dups"/>
75 <param name="output_format" value="9" /> 81 <param name="output_format" value="9" />
76 <output_collection name="genetrees_lists" type="list" count="4"> 82 <output_collection name="genetrees_lists" type="list" count="4">
77 <element name="1" file="11_genetree.nhx" ftype="nhx" /> 83 <element name="1" file="11_genetree.nhx" ftype="nhx" />
78 <element name="2" file="12_genetree.nhx" ftype="nhx" /> 84 <element name="2" file="12_genetree.nhx" ftype="nhx" />
79 <element name="3" file="13_genetree.nhx" ftype="nhx" /> 85 <element name="3" file="13_genetree.nhx" ftype="nhx" />
81 </output_collection> 87 </output_collection>
82 </test> 88 </test>
83 <test> 89 <test>
84 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 90 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
85 <param name="gene_node" value="0"/> 91 <param name="gene_node" value="0"/>
92 <param name="splitter" value="dups"/>
86 <param name="gainlose" value="True" /> 93 <param name="gainlose" value="True" />
87 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" /> 94 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
88 <param name="species_format" value="8" /> 95 <param name="species_format" value="8" />
89 <param name="output_format" value="9" /> 96 <param name="output_format" value="9" />
90 <output_collection name="genetrees_lists" type="list" count="5"> 97 <output_collection name="genetrees_lists" type="list" count="5">
91 <element name="1" file="21_genetree.nhx" ftype="nhx" /> 98 <element name="1" file="21_genetree.nhx" ftype="nhx" />
92 <element name="2" file="22_genetree.nhx" ftype="nhx" /> 99 <element name="2" file="22_genetree.nhx" ftype="nhx" />
93 <element name="3" file="23_genetree.nhx" ftype="nhx" /> 100 <element name="3" file="23_genetree.nhx" ftype="nhx" />
94 <element name="4" file="24_genetree.nhx" ftype="nhx" /> 101 <element name="4" file="24_genetree.nhx" ftype="nhx" />
95 <element name="5" file="25_genetree.nhx" ftype="nhx" /> 102 <element name="5" file="25_genetree.nhx" ftype="nhx" />
103 </output_collection>
104 </test>
105 <test>
106 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
107 <param name="gene_node" value="0"/>
108 <param name="splitter" value="treeko"/>
109 <param name="output_format" value="9" />
110 <output_collection name="genetrees_lists" type="list" count="5">
111 <element name="1" file="31_genetree.nhx" ftype="nhx" />
112 <element name="2" file="32_genetree.nhx" ftype="nhx" />
113 <element name="3" file="33_genetree.nhx" ftype="nhx" />
114 <element name="4" file="34_genetree.nhx" ftype="nhx" />
96 </output_collection> 115 </output_collection>
97 </test> 116 </test>
98 </tests> 117 </tests>
99 <help><![CDATA[ 118 <help><![CDATA[
100 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_. 119 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.