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comparison ete_genetree_splitter.xml @ 3:077021c45b96 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
author earlhaminst
date Mon, 12 Mar 2018 12:51:48 -0400
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2:03c10736e497 3:077021c45b96
1 <tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@.1">
2 <description>from a genetree using the ETE Toolkit</description>
3 <macros>
4 <import>ete_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <stdio>
8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" />
10 </stdio>
11 <command><![CDATA[
12 python '$__tool_directory__/ete_genetree_splitter.py'
13 --genetree '$genetreeFile'
14 --gene_node $gene_node
15 #if $gainlose_conditional.gainlose == "True"
16 --speciestree '$gainlose_conditional.speciesFile'
17 --species_format $gainlose_conditional.species_format
18 --gainlose
19 #end if
20 --output_format $output_format
21 ]]></command>
22 <inputs>
23 <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 <option value="0" selected="true">gene_species</option>
26 <option value="1">species_gene</option>
27 </param>
28 <conditional name="gainlose_conditional">
29 <param name="gainlose" type="select" label="Find out gene gain/lose">
30 <option value="True">Yes</option>
31 <option value="False" selected="true">No</option>
32 </param>
33 <when value="False" />
34 <when value="True">
35 <param name="speciesFile" type="data" format="nhx" label="Species file" help="Species Tree in nhx format" />
36 <param name="species_format" type="select" label="Input species tree format" help="See table below">
37 <option value="0">Flexible with support values (0)</option>
38 <option value="1">Flexible with internal node names (1)</option>
39 <option value="2">All branches + leaf names + internal supports (2)</option>
40 <option value="3">All branches + all names (3)</option>
41 <option value="4">Leaf branches + leaf names (4)</option>
42 <option value="5">Internal and leaf branches + leaf names (5)</option>
43 <option value="6">Internal branches + leaf names (6)</option>
44 <option value="7">Leaf branches + all names (7)</option>
45 <option value="8" selected="true">All names (8)</option>
46 <option value="9">Leaf names (9)</option>
47 <option value="100">Topology only (100)</option>
48 </param>
49 </when>
50 </conditional>
51
52 <param name="output_format" type="select" label="Output GeneTree format" help="See table below">
53 <option value="0">Flexible with support values (0)</option>
54 <option value="1">Flexible with internal node names (1)</option>
55 <option value="2">All branches + leaf names + internal supports (2)</option>
56 <option value="3">All branches + all names (3)</option>
57 <option value="4">Leaf branches + leaf names (4)</option>
58 <option value="5">Internal and leaf branches + leaf names (5)</option>
59 <option value="6">Internal branches + leaf names (6)</option>
60 <option value="7">Leaf branches + all names (7)</option>
61 <option value="8">All names (8)</option>
62 <option value="9" selected="true">Leaf names (9)</option>
63 <option value="100">Topology only (100)</option>
64 </param>
65 </inputs>
66 <outputs>
67 <collection name="genetrees_lists" type="list" label="${tool.name} on ${on_string}">
68 <discover_datasets pattern="(?P&lt;designation&gt;.+)_genetree\.nhx" ext="nhx" />
69 </collection>
70 </outputs>
71 <tests>
72 <test>
73 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
74 <param name="gene_node" value="0"/>
75 <param name="output_format" value="9" />
76 <output_collection name="genetrees_lists" type="list" count="4">
77 <element name="1" file="11_genetree.nhx" ftype="nhx" />
78 <element name="2" file="12_genetree.nhx" ftype="nhx" />
79 <element name="3" file="13_genetree.nhx" ftype="nhx" />
80 <element name="4" file="14_genetree.nhx" ftype="nhx" />
81 </output_collection>
82 </test>
83 <test>
84 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
85 <param name="gene_node" value="0"/>
86 <param name="gainlose" value="True" />
87 <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
88 <param name="species_format" value="8" />
89 <param name="output_format" value="9" />
90 <output_collection name="genetrees_lists" type="list" count="5">
91 <element name="1" file="21_genetree.nhx" ftype="nhx" />
92 <element name="2" file="22_genetree.nhx" ftype="nhx" />
93 <element name="3" file="23_genetree.nhx" ftype="nhx" />
94 <element name="4" file="24_genetree.nhx" ftype="nhx" />
95 <element name="5" file="25_genetree.nhx" ftype="nhx" />
96 </output_collection>
97 </test>
98 </tests>
99 <help><![CDATA[
100 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.
101
102 .. _ETE Toolkit: http://etetoolkit.org/
103
104 **Output format:**
105
106 ======= ============================================= ========================================================================================
107 FORMAT DESCRIPTION SAMPLE
108 ------- --------------------------------------------- ----------------------------------------------------------------------------------------
109 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);
110 1 flexible with internal node names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
111 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);
112 3 all branches + all names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
113 4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
114 5 internal and leaf branches + leaf names ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
115 6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788);
116 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
117 8 all names ((D,F)E,(B,H)B);
118 9 leaf names ((D,F),(B,H));
119 100 topology only ((,),(,));
120 ======= ============================================= ========================================================================================
121 ]]></help>
122 <expand macro="citations" />
123 </tool>