comparison TreeBest_best_wrapper.xml @ 0:4f9e5110914b draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
author earlhaminst
date Tue, 20 Dec 2016 16:32:25 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4f9e5110914b
1 <tool id="treebest_best_wrapper" name="TreeBeST best" version="1.9.2">
2 <description>Generate a phylogenetic tree using CDS alignment and species tree</description>
3 <requirements>
4 <requirement type="package" version="1.9.2_ep78">treebest</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" />
8 </stdio>
9 <command>
10 <![CDATA[
11 treebest best
12 -f $species_tree
13 $P
14 $S
15 $A
16 #if $C
17 -C $C
18 #end if
19 $s
20 $g
21 $N
22 -c $c
23 -d $d
24 -l $l
25 -L $L
26 -b $b
27 #if $k.k_selector == 'yes'
28 -k e
29 #else
30 -k $k.k_value
31 #end if
32 #if $a.a_selector == 'yes'
33 -a e
34 #else
35 -a $a.a_value
36 #end if
37 -F $F
38 -p "Galaxy_TreeBest_Best"
39 $aln
40 > $output
41 ]]>
42 </command>
43
44 <inputs>
45 <param name="species_tree" type="data" format="nhx" label="Species file in Newick format" help="-f"/>
46 <param name="aln" type="data" format="fasta" label="CDS alignment in FASTA format"/>
47 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip PHYML" help="(-P)" />
48 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Ignore the probability of gene evolution (NOT recommended)" help="(-S)" />
49 <param name="A" type="boolean" truevalue="-A" falsevalue="" label="Apply constraint to PHYML" help="(-A)" />
50 <param name="r" type="boolean" truevalue="-r" falsevalue="" label="Discard species that do not appear at all" help="(-r)" />
51 <param name="C" type="data" format="nhx" optional="true" label="Constraining tree" help="Optional (-C)" />
52 <param name="s" type="boolean" truevalue="-s" falsevalue="" label="Only build tree for genes from sequenced species" help="(-s)" />
53 <param name="g" type="boolean" truevalue="-g" falsevalue="" label="Collapse alternative splicing forms" help="(-g)" />
54 <param name="N" type="boolean" truevalue="-N" falsevalue="" label="Do not mask low-scoring segments" help="(-N)" />
55 <param name="F" type="integer" min="1" value="11" label="Quality cut-off" help="(-F)" />
56 <param name="c" type="integer" min="1" value="2" label="Number of rate categories for PHYML-HKY" help="(-c)" />
57 <conditional name="k">
58 <param name="k_selector" type="select" label="tv/ts ratio (kappa)" help="(-k)">
59 <option value="yes">Estimate (e)</option>
60 <option value="no">Specify value</option>
61 </param>
62 <when value="yes" />
63 <when value="no">
64 <param name="k_value" type="float" value="0.0" label="tv/ts ratio (kappa)" />
65 </when>
66 </conditional>
67 <conditional name="a">
68 <param name="a_selector" type="select" label="Alpha parameter for Gamma distribution" help="(-a)">
69 <option value="yes">Estimate (e)</option>
70 <option value="no">Specify value</option>
71 </param>
72 <when value="yes" />
73 <when value="no">
74 <param name="a_value" type="float" value="0.0" label="Alpha parameter for Gamma distribution" />
75 </when>
76 </conditional>
77 <param name="d" type="float" min="0" value="0.15" label="Duplication probability" help="(-d)" />
78 <param name="l" type="float" min="0" value="0.10" label="Probability of a loss following a speciation" help="(-l)" />
79 <param name="L" type="float" min="0" value="0.20" label="Probability of a loss following a duplication" help="(-L)" />
80 <param name="b" type="float" min="0" value="0.01" label="Probability of the presence of an inconsistent branch" help="(-b)" />
81 </inputs>
82
83 <outputs>
84 <data name="output" format="nhx" label="$tool.name on ${on_string}" />
85 </outputs>
86
87 <tests>
88 <test>
89 <param name="species_tree" ftype="nhx" value="species.nhx" />
90 <param name="aln" ftype="fasta" value="dna_alignment.fasta" />
91 <param name="F" value="11" />
92 <param name="k_selector" value="yes" />
93 <param name="a_selector" value="yes" />
94 <param name="d" value="0.15" />
95 <param name="l" value="0.10" />
96 <param name="L" value="0.20" />
97 <param name="b" value="0.01" />
98 <output name="output" file="genetree.nhx" />
99 </test>
100 </tests>
101 <help>
102 <![CDATA[
103 **What it does**
104
105 `TreeBeST`_ (gene Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.
106
107 The 'best' command builds the best gene tree from a species tree and a CDS alignment. The resultant tree will be bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses. Duplications and losses are also stored in the NHX format.
108
109 Note that TreeBeST first determines the topology of resultant tree with a complex procedure, and then performs a hundred times of resampling with an improved neighbour-joining algorithm. Branch lengths are finally estimated with the standard ML method under the HKY model.
110
111 .. _TreeBeST: http://treesoft.sourceforge.net/treebest.shtml
112 ]]>
113 </help>
114 <citations>
115 <citation type="doi">10.1080/10635150390235520</citation>
116 </citations>
117 </tool>