Mercurial > repos > boris > phylorelatives
comparison phylorelatives.xml @ 9:663fc7a8549b draft
uploaded tool xml
author | boris |
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date | Wed, 05 Jun 2013 14:05:16 -0400 |
parents | |
children | 034181b4b1b8 |
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8:e0638858594f | 9:663fc7a8549b |
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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.sequence}" | |
12 #end for | |
13 -m "${multifasta}" | |
14 -b "$iterations" | |
15 $pairwise | |
16 #if str($root.root_selector)=="upload_root": | |
17 -r "${root.root_fa}" | |
18 #end if | |
19 --relatives-out "$siblings" | |
20 --newick-out "$newick" | |
21 --trees-out "$plot" | |
22 | |
23 </command> | |
24 <inputs> | |
25 <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required"> | |
26 <param format="fasta" name="sequence" type="data" label="FASTA file" help="Requires at least one minor allele sequence properly labeled "_minor" or "_test" e.g. ">sample1_minor""> | |
27 </param> | |
28 </repeat> | |
29 <conditional name="root"> | |
30 <param name="root_selector" type="select" label=" Root sequence"> | |
31 <option value="unrooted" selected="True"></option> | |
32 <option value="upload_root"></option> | |
33 </param> | |
34 <when value="unrooted"> | |
35 </when> | |
36 <when value="upload_root"> | |
37 <param name="root_fa" format="fasta" type="data" label="Root tree using" help="Must have the same length as input sequences"/> | |
38 </when> | |
39 </conditional> | |
40 <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to "Complete deletion""/> | |
41 <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> | |
42 </inputs> | |
43 <outputs> | |
44 <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" /> | |
45 <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/> | |
46 <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/> | |
47 <data format="png" name="plot" label="${tool.name} on ${on_string}: plot"/> | |
48 </outputs> | |
49 <tests> | |
50 <test> | |
51 <param name="iterations" value="0"/> | |
52 <param name="sequence" value="test.fa"/> | |
53 <output name="siblings" file="test.fa-siblings.tab"/> | |
54 </test> | |
55 </tests> | |
56 | |
57 <help> | |
58 | |
59 | |
60 | |
61 | |
62 (boris-at-bx.psu.edu) | |
63 | |
64 | |
65 ----- | |
66 | |
67 .. class:: infomark | |
68 | |
69 **What it does** | |
70 | |
71 Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. | |
72 One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor). | |
73 It returns the FASTA multiple alignment used, and reports a table with the relatives of the minor allele sequence in a NJ tree, the tree plot and newick string. | |
74 | |
75 ----- | |
76 | |
77 .. class:: warningmark | |
78 | |
79 **Note** | |
80 | |
81 This tools DOES NOT align the sequences. | |
82 The FASTA multiple alignment file is fabricated by concatenating same length homologous sequences. | |
83 An independently aligned FASTA multiple alignment file can be used as well. | |
84 | |
85 ----- | |
86 | |
87 .. class:: infomark | |
88 | |
89 **About formats** | |
90 | |
91 **FASTA multiple alignment** -- | |
92 | |
93 describe format shortly | |
94 | |
95 ----- | |
96 | |
97 **Example** | |
98 | |
99 - For the following dataset:: | |
100 >sample1_major | |
101 >sample1_minor | |
102 >sample2_major | |
103 >sample3_major | |
104 >sample4_major | |
105 | |
106 | |
107 - running this tool with **b = 1000** **m = yes** **root = RSRS**, will return:: | |
108 newick | |
109 relatives | |
110 plot | |
111 </help> | |
112 | |
113 </tool> |