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comparison ete_mod.xml @ 2:03c10736e497 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
author earlhaminst
date Tue, 07 Nov 2017 11:45:13 -0500
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1:a4ba317fc713 2:03c10736e497
1 <tool id="ete3_mod" name="ETE mod" version="@VERSION@">
2 <description>manipulates tree topology by rooting, pruning or sorting branches</description>
3 <macros>
4 <import>ete_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ete3 mod -t
9 #for $input_tree in $input_trees:
10 '$input_tree'
11 #end for
12 -v '$verbosity'
13 #if $outgroup:
14 --outgroup '$outgroup'
15 #end if
16 ## #if float($ultrametric) > 0.0:
17 ## --ultrametric $ultrametric
18 ## #end if
19 #if $prune:
20 #set node_list = "'" + "' '".join($prune.split(',')) + "'"
21 --prune $node_list
22 #end if
23 $prune_preserve_lengths
24 $unroot
25 $sort_branches
26 $ladderize
27 $resolve_polytomies
28 $standardize
29 > '$output_tree'
30 ]]></command>
31 <inputs>
32 <param name="input_trees" argument="-t" type="data" format="nhx" multiple="true" label="Newick trees" />
33 <param name="verbosity" argument="-v" type="integer" value="0" min="0" max="4" label="Verbosity level"
34 help="0=totally quite, 1=errors only, 2=warning+errors, 3=info+warnings+errors 4=debug (-v)" />
35 <param argument="--outgroup" type="text" value="" label="Reroot tree with outgroup (space separated list of leaf names)"
36 help="Root the tree using the provided outgroup. If several
37 names are provided, the first common ancestor grouping
38 all of them will be selected as outgroup" />
39 <!-- parameter does not work in the current version
40 <param argument="- -ultrametric" type="float" value="0" min="0" label="Convert tree into ultrametric"
41 help="Convert tree into ultrametric (all leaves have the
42 same distance to root). If an argument (!=0) is provided, it
43 will be used as the expected tree length" />-->
44 <param argument="--prune" type="text" value="" label="Prune nodes from the tree (comma-separated list of leaf names)"
45 help="Remove all nodes in the tree except the ones provided (empty does not prune)" />
46 <param argument="--prune_preserve_lengths" type="boolean" truevalue="--prune_preserve_lengths" falsevalue="" label="Prune: preserve length"
47 help="Branch lengths of the removed nodes are added to the kept branches, thus preserving original tree length" />
48 <param argument="--unroot" type="boolean" truevalue="--unroot" falsevalue="" label="Unroots the tree" />
49 <param argument="--sort_branches" type="boolean" truevalue="--sort_branches" falsevalue="" label="Sort branches"
50 help="Sort branches according to node names" />
51 <param argument="--ladderize" type="boolean" truevalue="--ladderize" falsevalue="" label="Ladderize"
52 help="Sort branches by partition size" />
53 <param argument="--resolve_polytomies" type="boolean" truevalue="--resolve_polytomies" falsevalue="" label="Resolve polytomies"
54 help="Converts polytomies into bifurcations" />
55 <param argument="--standardize" type="boolean" truevalue="--standardize" falsevalue="" label="Standardize tree"
56 help="Standardize tree topology by expanding polytomies and single child nodes" />
57 </inputs>
58 <outputs>
59 <data name="output_tree" format="nhx" label="${tool.name} on ${on_string}"/>
60 </outputs>
61 <tests>
62 <test>
63 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
64 <param name="outgroup" value="A" />
65 <output name="output_tree" file="tree1_ogA.nhx" />
66 </test>
67 <test>
68 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
69 <param name="prune" value="A,C" />
70 <output name="output_tree" file="tree1_pruneAC.nhx" />
71 </test>
72 <test>
73 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
74 <param name="prune" value="A,C" />
75 <param name="prune_preserve_lengths" value="--prune_preserve_lengths" />
76 <output name="output_tree" file="tree1_pruneACpreserve.nhx" />
77 </test>
78 <test>
79 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
80 <param name="unroot" value="--unroot" />
81 <output name="output_tree" file="tree1_unroot.nhx" />
82 </test>
83 <test>
84 <param name="input_trees" ftype="nhx" value="tree2.nhx" />
85 <param name="sort_branches" value="--sort_branches" />
86 <output name="output_tree" file="tree2_sort.nhx" />
87 </test>
88 <test>
89 <param name="input_trees" ftype="nhx" value="tree1.nhx" />
90 <param name="ladderize" value="--ladderize" />
91 <output name="output_tree" file="tree1_ladder.nhx" />
92 </test>
93 <test>
94 <param name="input_trees" ftype="nhx" value="tree1_unroot.nhx" />
95 <param name="resolve_polytomies" value="--resolve_polytomies" />
96 <output name="output_tree" file="tree1_unroot_resolve.nhx" />
97 </test>
98 <test>
99 <param name="input_trees" ftype="nhx" value="tree3.nhx" />
100 <param name="standardize" value="--standardize" />
101 <output name="output_tree" file="tree3_stand.nhx" />
102 </test>
103 </tests>
104 <help><![CDATA[
105 Modify a given input tree using the etetoolkit: http://etetoolkit.org/
106 ]]></help>
107 <expand macro="citations" />
108 </tool>