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