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author boris
date Mon, 03 Feb 2014 13:01:44 -0500
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1 <tool id="phylorelatives" name="Phylorelatives" version="0.0.1">
2 <description>Relatedness of minor alelle sequences in NJ tree</description>
3 <requirements>
4 <requirement type="package" version="2.15.0">R</requirement>
5 <requirement type="package" version="2.2.6">rpy2</requirement>
6 <requirement type="package" version="3.12.0">dendropy</requirement>
7 <requirement type="package" version="3.0-8">ape</requirement>
8 </requirements>
9 <command interpreter="python">phylorelatives.py
10 #for $sequence in ( $sequences ):
11 -i "${sequence}"
12 #end for
13 -m "${multifasta}"
14 -b "$iterations"
15 $pairwise
16 $major_only
17 #if str($root.root_selector)=="add_root":
18 -r "${root.root_fa}"
19 #end if
20 --relatives-out "$siblings"
21 --newick-out "$newick"
22 --trees-out "$plot"
23 </command>
24 <inputs>
25 <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
26 </param>
27 <conditional name="root">
28 <param name="root_selector" type="select" label=" Root sequence">
29 <option value="unrooted" selected="True"></option>
30 <option value="add_root"></option>
31 </param>
32 <when value="unrooted">
33 </when>
34 <when value="add_root">
35 <param name="root_fa" format="fasta" type="data" label="Root tree using" help="Must have the same length as input sequences"/>
36 </when>
37 </conditional>
38 <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to &quot;Complete deletion&quot;"/>
39 <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>
40 <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="All sequences will be treated as major allele sequences. Useful to generate background tree"/>
41 </inputs>
42 <outputs>
43 <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta used" />
44 <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives list"/>
45 <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/>
46 <data format="png" name="plot" label="${tool.name} on ${on_string}: tree plot"/>
47 </outputs>
48 <tests>
49 <test>
50 <param name="iterations" value="0"/>
51 <param name="sequences" value="test.fa"/>
52 <output name="siblings" file="test.fa-siblings.tab"/>
53 </test>
54 </tests>
55
56 <help>
57
58
59
60 The major and minor allele sequences of a sample are expected to cluster together in a phylogenetic tree.
61 Deviation from expectation suggests potential contamination coming from the closest unrelated samples.
62
63 -----
64
65 .. class:: infomark
66
67 **What it does**
68
69 Constructs relatedness of a set of sequences based on the pairwise proportion of different sites.
70 One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor).
71 It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives, the tree plot and newick string of the tree.
72
73 -----
74
75 .. class:: warningmark
76
77 **Note**
78
79 This tools DOES NOT align the sequences.
80 Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files.
81
82 -----
83
84 .. class:: infomark
85
86 **About formats**
87
88 *FASTA multiple alignment*
89
90 See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
91
92 *Newick*
93
94 http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm
95
96 -----
97
98 **Example**
99
100 - For the multiple alignment composed of the following FASTA files::
101
102 >sample1_major
103 >sample1_minor
104 >sample2_major
105 >sample3_major
106 >sample4_major
107
108
109 - running this tool with *root = RSRS.fasta*, and default parameters will return four datasets::
110
111 1. multiple alignment file used for running the tool
112 2. relatives of sample1_minor
113 3. NJ tree newick string (rooted on RSRS)
114 4. NJ tree png plot (rooted on RSRS)
115
116 -----
117
118 **Citation**
119
120 If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.*
121 (boris-at-bx.psu.edu)
122
123 </help>
124
125 </tool>