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1 <tool id="MAF_To_BED1" name="Maf to BED" force_history_refresh="True">
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2 <description>Converts a MAF formatted file to the BED format</description>
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3 <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks $__new_file_path__</command>
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4 <inputs>
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5 <param format="maf" name="input1" type="data" label="MAF file to convert"/>
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6 <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species">
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7 <options>
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8 <filter type="data_meta" ref="input1" key="species" />
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9 </options>
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10 </param>
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11 <param name="complete_blocks" type="select" label="Exclude blocks which have a requested species missing">
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12 <option value="partial_allowed">include blocks with missing species</option>
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13 <option value="partial_disallowed">exclude blocks with missing species</option>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="bed" name="out_file1" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input1" value="4.maf"/>
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22 <param name="species" value="hg17"/>
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23 <param name="complete_blocks" value="partial_disallowed"/>
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24 <output name="out_file1" file="cf_maf_to_bed.dat"/>
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25 </test>
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26 </tests>
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27 <help>
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28
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29 **What it does**
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30
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31 This tool converts every MAF block to an interval line (in BED format; scroll down for description of MAF and BED formats) describing position of that alignment block within a corresponding genome.
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32
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33 The interface for this tool contains two pages (steps):
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34
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35 * **Step 1 of 2**. Choose multiple alignments from history to be converted to BED format.
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36 * **Step 2 of 2**. Choose species from the alignment to be included in the output and specify how to deal with alignment blocks that lack one or more species:
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37
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38 * **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (only reference genome, shown in **bold**, is selected by default). If you select more than one species, then more than one history item will be created.
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39 * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below).
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40
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41
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42 -----
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43
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44 **Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
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45
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46 For the following alignment::
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47
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48 ##maf version=1
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49 a score=68686.000000
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50 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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51 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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52 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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53 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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54 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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55
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56 a score=10289.000000
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57 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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58 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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59 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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60
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61 the tool will create **a single** history item containing the following (**note** that field 4 is added to the output and is numbered iteratively: hg18_0, hg18_1 etc.)::
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62
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63 chr20 56827368 56827443 hg18_0 0 +
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64 chr20 56827443 56827480 hg18_1 0 +
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65
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66 -----
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67
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68 **Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
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69
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70 For the following alignment::
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71
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72 ##maf version=1
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73 a score=68686.000000
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74 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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75 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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76 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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77 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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78 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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79
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80 a score=10289.000000
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81 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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82 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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83 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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84
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85 the tool will create **two** history items (one for hg18 and one fopr mm8) containing the following (**note** that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):
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86
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87 History item **1** (for hg18)::
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88
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89 chr20 56827368 56827443 hg18_0 0 +
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90
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91 History item **2** (for mm8)::
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92
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93 chr2 173910832 173910893 mm8_0 0 +
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94
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95 -------
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96
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97 .. class:: infomark
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98
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99 **About formats**
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100
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101 **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
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102
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103 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
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104 - Each sequence in an alignment is on a single line.
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105 - Lines starting with # are considered to be comments.
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106 - Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment.
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107 - Some MAF files may contain two optional line types:
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108
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109 - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
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110 - An "e" line containing information about the size of the gap between the alignments that span the current block.
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111
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112 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and a number of additional optional ones:
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113
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114 The first three BED fields (required) are::
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115
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116 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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117 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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118 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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119
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120 Additional (optional) fields are::
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121
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122 4. name - The name of the BED line.
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123 5. score - A score between 0 and 1000.
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124 6. strand - Defines the strand - either '+' or '-'.
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125
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126 ------
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127
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128 **Citation**
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129
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130 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_
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131
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132
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133 </help>
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134 <code file="maf_to_bed_code.py"/>
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135 </tool>
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136
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