Mercurial > repos > earlhaminst > ete

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