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annotate getalleleseq/getalleleseq.xml @ 1:c16e440a53a0 draft

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Changed xml to handle multiple output from current directory instead
author boris
date Tue, 18 Mar 2014 09:51:31 -0400
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1 <tool id="getalleleseq" name="FASTA from allele counts" version="0.0.1" force_history_refresh="True">
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2 <description>Generate major and minor allele sequences from alleles table</description>
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3 <command interpreter="python">getalleleseq.py
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4 $alleles
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5 -l $seq_length
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6 -j $major_seq
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7 -p $major_seq.id
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8 </command>
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9 <inputs>
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10 <param format="tabular" name="alleles" type="data" label="Table containing major and minor alleles base per position" help="must be tabular and follow the Variant Annotator tool output format"/>
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11 <param name="seq_length" type="integer" value="16569" label="Background sequence length" help="e.g. 16569 for mitochondrial variants"/>
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12 </inputs>
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13 <outputs>
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14 <data format="fasta" name="major_seq"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="alleles" value="test-table-getalleleseq.tab"/>
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19 <param name="seq_length" value="16569"/>
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20 <output name="major_seq" file="test-major-allele-out-getalleleseq.fa"/>
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21 </test>
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22 </tests>
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23
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24 <help>
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25
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26
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27 The major allele sequence of a sample is simply the sequence consisting of the most frequent nucleotide per position.
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28 Replacing the major allele for the second most frequent allele at diploid positions generates the minor allele sequence.
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29
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30 -----
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31
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32 .. class:: infomark
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33
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34 **What it does**
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35
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36 It takes the table generated from the Variant Annotator tool to derive a major and minor allele sequence per sample.
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37 Since all sequences share the same length all the major allele sequences are included into a single file (with proper headers per sample)
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38 to create a multiple sequence alignment in FASTA format that can be used for downstream phylogenetic analyses.
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39 In contrast, the minor allele sequences are informed as single FASTA files per sample to ease their downstream manipulation.
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40
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41 -----
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42
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43 .. class:: warningmark
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44
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45 **Note**
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46
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47 Please, follow the format described below for the input file:
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48
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49 -----
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50
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51 .. class:: infomark
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52
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53 **Formats**
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54
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55 **Variant Annotator tool output format**
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56
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57 Columns::
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58
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59 1. sample id
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60 2. chromosome
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61 3. position
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62 4 counts for A's
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63 5. counts for C's
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64 6. counts for G's
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65 7. counts for T's
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66 8. Coverage
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67 9. Number of alleles passing frequency threshold
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68 10. Major allele
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69 11. Minor allele
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70 12. Minor allele frequency in position
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71
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72
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73 **FASTA multiple alignment**
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74
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75 See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
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76
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77 -----
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78
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79 **Example**
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80
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81 - For the following dataset::
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82
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83 S9 chrM 3 3 0 2 214 219 0 T A 0.013698630137
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84 S9 chrM 4 3 249 3 0 255 0 C N 0.0
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85 S9 chrM 5 245 1 1 0 247 1 A N 0.0
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86 S11 chrM 6 0 292 0 0 292 1 C . 0.0
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87 S7 chrM 6 0 254 0 0 254 1 C . 0.0
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88 S9 chrM 6 2 306 2 0 310 0 C N 0.0
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89 S11 chrM 7 281 0 3 0 284 0 A G 0.0105633802817
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90 S7 chrM 7 249 0 2 0 251 1 A G 0.00796812749004
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91 etc. for all covered positions per sample...
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92
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93 - Running this tool with background sequence length 16569 will produce 4 files::
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94
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95 1. Multiple alignment FASTA file containing the major allele sequences of samples S7, S9 and S11
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96 2. minor allele sequence of sample S7
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97 3. minor allele sequence of sample S9
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98 4. minor allele sequence of sample S11
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99
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100 -----
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101
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102 **Citation**
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103
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104 If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al (2014). *Acccepted in Biotechniques*
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105 (boris-at-bx.psu.edu)
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106
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107 </help>
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108 </tool>