Mercurial > repos > earlhaminst > ete
comparison ete_genetree_splitter.xml @ 9:b29ee6a16524 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
author | earlhaminst |
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date | Tue, 20 Oct 2020 15:10:40 +0000 |
parents | f1eca1158f21 |
children | 541a2ffc01ff |
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8:16e925bf567e | 9:b29ee6a16524 |
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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`_. |