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comparison ete_tree_generator.xml @ 0:276e3ee68c37 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
author earlhaminst
date Thu, 15 Dec 2016 12:55:02 -0500
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1 <tool id="species_tree_generator" name="Species tree generator" version="3.0.0b35">
2 <description>from a list of species using the ETE Toolkit</description>
3 <requirements>
4 <requirement type="package" version="3.0.0b35">ete3</requirement>
5 </requirements>
6 <stdio>
7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" />
9 </stdio>
10 <command>
11 <![CDATA[
12 python $__tool_directory__/ete_tree_generator.py
13 -s '$speciesFile'
14 #if $output_format.treebest == 'yes'
15 -f 8
16 #else
17 -f ${output_format.format_selector}
18 #end if
19 -t $output_format.treebest
20 -d $database
21 ]]>
22 </command>
23 <inputs>
24 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
25 <conditional name="output_format">
26 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
27 <option value="yes">Yes</option>
28 <option value="no" selected="true">No</option>
29 </param>
30 <when value="yes" />
31 <when value="no">
32 <param name="format_selector" type="select" label="Output format" help="See table below">
33 <option value="0" selected="true">Flexible with support values (0)</option>
34 <option value="1">Flexible with internal node names (1)</option>
35 <option value="2">All branches + leaf names + internal supports (2)</option>
36 <option value="3">All branches + all names (3)</option>
37 <option value="4">Leaf branches + leaf names (4)</option>
38 <option value="5">Internal and leaf branches + leaf names (5)</option>
39 <option value="6">Internal branches + leaf names (6)</option>
40 <option value="7">Leaf branches + all names (7)</option>
41 <option value="8">All names (8)</option>
42 <option value="9">Leaf names (9)</option>
43 <option value="100">Topology only (100)</option>
44 </param>
45 </when>
46 </conditional>
47 <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
48 <option value="no" selected="true">No</option>
49 <option value="yes">Yes</option>
50 </param>
51 </inputs>
52 <outputs>
53 <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/>
54 </outputs>
55 <tests>
56 <test>
57 <param name="speciesFile" ftype="txt" value="species.txt" />
58 <param name="treebest" value="yes" />
59 <output name="outputFile" file="out.nhx" />
60 </test>
61 </tests>
62 <help>
63 <![CDATA[
64 Generate a species tree from a list of species using the `ETE Toolkit`_.
65
66 .. _ETE Toolkit: http://etetoolkit.org/
67
68 **Output format:**
69
70 ======= ============================================= ========================================================================================
71 FORMAT DESCRIPTION SAMPLE
72 ------- --------------------------------------------- ----------------------------------------------------------------------------------------
73 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);
74 1 flexible with internal node names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
75 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);
76 3 all branches + all names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
77 4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
78 5 internal and leaf branches + leaf names ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
79 6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788);
80 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
81 8 all names ((D,F)E,(B,H)B);
82 9 leaf names ((D,F),(B,H));
83 100 topology only ((,),(,));
84 ======= ============================================= ========================================================================================
85 ]]>
86 </help>
87 <citations>
88 <citation type="doi">10.1093/molbev/msw046</citation>
89 </citations>
90 </tool>