Mercurial > repos > earlhaminst > ete

comparison ete_genetree_splitter.xml @ 12:dc32007a6b36 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
author earlhaminst
date Tue, 07 Jun 2022 08:58:05 +0000
parents 541a2ffc01ff
children d40b9a7debe5
comparison
equal deleted inserted replaced
11:2db72467da51 12:dc32007a6b36
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 --split $splitting_conditional.splitter
16 #if $gainlose_conditional.gainlose == "True" 16 #if $gainlose_conditional.gainlose == "True"
17 --speciestree '$gainlose_conditional.speciesFile' 17 --speciestree '$gainlose_conditional.speciesFile'
18 --species_format $gainlose_conditional.species_format 18 --species_format $gainlose_conditional.species_format
19 --gainlose 19 --gainlose
20 #end if 20 #end if
21 #if $splitting_conditional.splitter == "species"
22 --ingroup '$splitting_conditional.ingroup'
23 --outgroup '$splitting_conditional.outgroup'
24 #end if
21 --output_format $output_format 25 --output_format $output_format
22 ]]></command> 26 ]]></command>
23 <inputs> 27 <inputs>
24 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" /> 28 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" />
25 <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option"> 29 <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option">
26 <option value="0" selected="true">gene_species</option> 30 <option value="0" selected="true">gene_species</option>
27 <option value="1">species_gene</option> 31 <option value="1">species_gene</option>
28 </param> 32 </param>
29 <param name="splitter" type="select" label="GeneTree splitting algorithm"> 33 <conditional name="splitting_conditional">
30 <option value="dups">Split by Duplication</option> 34 <param name="splitter" type="select" label="GeneTree splitting algorithm">
31 <option value="treeko">Split using TreeKO algorithm</option> 35 <option value="dups">Split by Duplication</option>
32 </param> 36 <option value="treeko">Split using TreeKO algorithm</option>
37 <option value="species">Split using In-group and Out-group species</option>
38 </param>
39 <when value="dups" />
40 <when value="treeko" />
41 <when value="species">
42 <param name="ingroup" type="text" label="In-group species list" help="Comma-separated species list without whitespaces or special characters" />
43 <param name="outgroup" type="text" label="Out-group species list" help="Comma-separated species list without whitespaces or special characters" />
44 </when>
45 </conditional>
33 <conditional name="gainlose_conditional"> 46 <conditional name="gainlose_conditional">
34 <param name="gainlose" type="select" label="Find out gene gain/lose"> 47 <param name="gainlose" type="select" label="Find out gene gain/lose">
35 <option value="True">Yes</option> 48 <option value="True">Yes</option>
36 <option value="False" selected="true">No</option> 49 <option value="False" selected="true">No</option>
37 </param> 50 </param>
105 <test> 118 <test>
106 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> 119 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
107 <param name="gene_node" value="0"/> 120 <param name="gene_node" value="0"/>
108 <param name="splitter" value="treeko"/> 121 <param name="splitter" value="treeko"/>
109 <param name="output_format" value="9" /> 122 <param name="output_format" value="9" />
110 <output_collection name="genetrees_lists" type="list" count="5"> 123 <output_collection name="genetrees_lists" type="list" count="4">
111 <element name="1" file="31_genetree.nhx" ftype="nhx" /> 124 <element name="1" file="31_genetree.nhx" ftype="nhx" />
112 <element name="2" file="32_genetree.nhx" ftype="nhx" /> 125 <element name="2" file="32_genetree.nhx" ftype="nhx" />
113 <element name="3" file="33_genetree.nhx" ftype="nhx" /> 126 <element name="3" file="33_genetree.nhx" ftype="nhx" />
114 <element name="4" file="34_genetree.nhx" ftype="nhx" /> 127 <element name="4" file="34_genetree.nhx" ftype="nhx" />
128 </output_collection>
129 </test>
130
131 <test>
132 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
133 <param name="gene_node" value="0"/>
134 <param name="splitter" value="species"/>
135 <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
136 <param name="outgroup" value="susscrofa" />
137 <param name="output_format" value="9" />
138 <output_collection name="genetrees_lists" type="list" count="4">
139 <element name="1" file="41_genetree.nhx" ftype="nhx" />
140 <element name="2" file="42_genetree.nhx" ftype="nhx" />
141 <element name="3" file="43_genetree.nhx" ftype="nhx" />
142 <element name="4" file="44_genetree.nhx" ftype="nhx" />
115 </output_collection> 143 </output_collection>
116 </test> 144 </test>
117 </tests> 145 </tests>
118 <help><![CDATA[ 146 <help><![CDATA[
119 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_. 147 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.