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1 <tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0">
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2 <description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description>
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3 <command interpreter="perl">
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4 microsatellite_birthdeath.pl
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5 $alignment
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6 $orthfile
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7 $outfile
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8 $species
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9 "$tree_definition"
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10 $thresholds
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11 $separation
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12 $simthresh
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13
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14 </command>
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15 <inputs>
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16 <page>
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17 <param format="maf" name="alignment" type="data" label="Select MAF alignments that have NOT been masked for nucleotide quality"/>
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18
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19 <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>
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20
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21 <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
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22 <options>
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23 <filter type="data_meta" ref="alignment" key="species" />
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24 </options>
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25 </param>
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26
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27 <param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction"
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28 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
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29
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30 <param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
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31 help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/>
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32
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33 <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
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34 help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/>
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35
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36 <param name="simthresh" size="10" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance"
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37 help="Enter a value from 0 to 100"/>
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38
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39
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40 </page>
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41 </inputs>
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42 <outputs>
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43 <data format="txt" name="outfile" metadata_source="orthfile"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="alignment" value="regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz"/>
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48 <param name="orthfile" value="regVariation/microsatellite/Galaxy17_short_raw.txt"/>
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49 <param name="thresholds" value="9,10,12,12"/>
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50 <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
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51 <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
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52 <param name="separation" value="10"/>
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53 <param name="simthresh" value="85"/>
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54 <output name="outfile" file="regVariation/microsatellite/Galaxy17_unmasked_results.txt"/>
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55 </test>
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56 </tests>
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57
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58
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59 <help>
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60
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61 .. class:: infomark
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62
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63 **What it does**
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64
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65 This tool uses raw orthologous microsatellite clusters (identified by the tool "Extract orthologous microsatellites") to identify microsatellite births and deaths along individual lineages of a phylogenetic tree.
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66 -----
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67
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68 .. class:: warningmark
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69
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70 **Note**
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71
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72 A tab-separated output table (depending on the species being considered) is generated where each row contains all information for a microsatellite locus from multiple species.
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73 The table typically reads like this:
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74
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75 hg18.chr22 16153057 16153074 A 1 ins=,imot:0:tt;dels= ,9:t>c -panTro2 hg18:tttttttttttttttttt,ponAbe2:--tttttttttttttttt,panTro2:-----ttttctttttttt
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76
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77 hg18.chr22 16131711 16131722 ATGC 4 NA ,2:C>T +ponAbe2 hg18:CACGCATGCATG,ponAbe2:CATGCATGCATG,panTro2:CACGCATGCATG,rheMac2:CACGCGTGCATG
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78
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79 Where columns list the following:
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80
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81 1: Chromosome/scaffold/contig of one of the species. The species chosen is the first species readable in the Newick tree submitted by the user.
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82
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83 2: Start coordinate
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84
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85 3: End coordinate
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86
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87 4: Motif of microsatellite
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88
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89 5: Motif size
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90
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91 6: Insertion and deletion details. Insertions are separated from deletions by a ";", and individual insertions and deletions are separated from others by a comma. For the purpose of illustration, consider the first row listed above:
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92 "imot:0:tt", where imot/imotf again suggest insertion, the number indicates position of insertion within the microsatellite's alignment, and this is followed by identity of nucleotides that are inserted.
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93
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94 7: Substitution details. Individual substitutions are separated by commas. Each entry contains the position of substitution event in the microsatellites' alignment, and the nature of substitution.
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95
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96 8: Inference of birth/death event. Births are indicated by "+", and deaths by "-". Events such as "-hg18:panTro2" suggest death in the common ancestor of hg18 and panTro2, whereas events such as "-hg18.panTro2" indicate parallel, independent death events along the two lineages. Alternative interpretations of the event may also be listed, following a "/", such as:
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97 "+hg18.+panTro2 / +hg18:panTro2"
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98
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99 9: Actual sequences in the alignment, separated by commas.
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100
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101 </help>
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102
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103
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104 </tool>
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