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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.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 $pairwise
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16 #if str($root.root_selector)=="upload_root":
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17 -r "${root.root_fa}"
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18 #end if
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19 --relatives-out "$siblings"
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20 --newick-out "$newick"
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21 --trees-out "$plot"
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22
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23 </command>
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24 <inputs>
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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">
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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"">
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27 </param>
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28 </repeat>
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29 <conditional name="root">
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30 <param name="root_selector" type="select" label=" Root sequence">
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31 <option value="unrooted" selected="True"></option>
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32 <option value="upload_root"></option>
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33 </param>
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34 <when value="unrooted">
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35 </when>
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36 <when value="upload_root">
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37 <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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38 </when>
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39 </conditional>
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40 <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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41 <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>
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42 </inputs>
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43 <outputs>
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44 <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" />
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45 <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/>
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46 <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/>
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47 <data format="png" name="plot" label="${tool.name} on ${on_string}: plot"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="iterations" value="0"/>
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52 <param name="sequence" value="test.fa"/>
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53 <output name="siblings" file="test.fa-siblings.tab"/>
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54 </test>
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55 </tests>
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56
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57 <help>
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58
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59
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60
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61
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62 (boris-at-bx.psu.edu)
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63
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64
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65 -----
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66
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67 .. class:: infomark
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68
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69 **What it does**
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70
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71 Constructs relatedness of a set of sequences based on the pairwise proportion of different sites.
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72 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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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.
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74
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75 -----
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76
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77 .. class:: warningmark
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78
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79 **Note**
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80
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81 This tools DOES NOT align the sequences.
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82 The FASTA multiple alignment file is fabricated by concatenating same length homologous sequences.
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83 An independently aligned FASTA multiple alignment file can be used as well.
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84
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85 -----
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86
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87 .. class:: infomark
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88
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89 **About formats**
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90
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91 **FASTA multiple alignment** --
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92
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93 describe format shortly
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94
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95 -----
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96
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97 **Example**
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98
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99 - For the following dataset::
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100 >sample1_major
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101 >sample1_minor
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102 >sample2_major
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103 >sample3_major
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104 >sample4_major
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105
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106
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107 - running this tool with **b = 1000** **m = yes** **root = RSRS**, will return::
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108 newick
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109 relatives
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110 plot
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111 </help>
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112
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113 </tool> |
