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1 <tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1">
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2 <description>Converts a MAF formatted file to FASTA format</description>
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3 <command interpreter="python">
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4 #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks
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5 #else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1
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6 #end if#
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7 </command>
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8 <inputs>
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9 <param format="maf" name="input1" type="data" label="MAF file to convert"/>
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10 <conditional name="fasta_target_type">
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11 <param name="fasta_type" type="select" label="Type of FASTA Output">
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12 <option value="multiple" selected="true">Multiple Blocks</option>
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13 <option value="concatenated">One Sequence per Species</option>
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14 </param>
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15 <when value="multiple">
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16 <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="checked taxa will be included in the output">
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17 <options>
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18 <filter type="data_meta" ref="input1" key="species" />
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19 </options>
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20 </param>
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21 <param name="complete_blocks" type="select" label="Choose to">
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22 <option value="partial_allowed">include blocks with missing species</option>
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23 <option value="partial_disallowed">exclude blocks with missing species</option>
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24 </param>
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25 </when>
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26 <when value="concatenated">
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27 <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true">
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28 <options>
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29 <filter type="data_meta" ref="input1" key="species" />
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30 </options>
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31 </param>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="fasta" name="out_file1" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input1" value="3.maf" ftype="maf"/>
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41 <param name="fasta_type" value="concatenated"/>
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42 <param name="species" value="canFam1"/>
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43 <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>
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44 </test>
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45 <test>
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46 <param name="input1" value="4.maf" ftype="maf"/>
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47 <param name="fasta_type" value="multiple"/>
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48 <param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/>
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49 <param name="complete_blocks" value="partial_allowed"/>
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50 <output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/>
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51 </test>
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52 </tests>
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53 <help>
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54
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55 **Types of MAF to FASTA conversion**
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56
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57 * **Multiple Blocks** converts a single MAF block to a single FASTA block. For example, if you have 6 MAF blocks, they will be converted to 6 FASTA blocks.
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58 * **One Sequence per Species** converts MAF blocks to a single aggregated FASTA block. For example, if you have 6 MAF blocks, they will be converted and concatenated into a single FASTA block.
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59
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60 -------
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61
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62 **What it does**
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63
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64 This tool converts MAF blocks to FASTA format and concatenates them into a single FASTA block or outputs multiple FASTA blocks separated by empty lines.
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65
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66 The interface for this tool contains two pages (steps):
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67
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68 * **Step 1 of 2**. Choose multiple alignments from history to be converted to FASTA format.
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69 * **Step 2 of 2**. Choose the type of output as well as the species from the alignment to be included in the output.
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70
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71 Multiple Block output has additional options:
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72
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73 * **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 (all species are selected by default).
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74 * **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 such a block **will not** be included in the output (see **Example 2** below). For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned.
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75
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76
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77 -----
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78
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79 **Example 1**:
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80
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81 In the concatenated approach, the following alignment::
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82
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83 ##maf version=1
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84 a score=68686.000000
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85 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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86 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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87 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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88 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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89 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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90
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91 a score=10289.000000
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92 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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93 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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94 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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95
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96 will be converted to (**note** that because mm8 (mouse) and canFam2 (dog) are absent from the second block, they are replaced with gaps after concatenation)::
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97
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98 >canFam2
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99 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C-------------------------------------
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100 >hg18
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101 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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102 >mm8
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103 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC--------------------------------------------
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104 >panTro2
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105 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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106 >rheMac2
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107 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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108
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109 ------
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110
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111 **Example 2a**: Multiple Block Approach **Include all species** and **include blocks with missing species**:
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112
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113 The following alignment::
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114
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115 ##maf version=1
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116 a score=68686.000000
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117 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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118 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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119 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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120 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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121 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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122
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123 a score=10289.000000
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124 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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125 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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126 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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127
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128 will be converted to::
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129
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130 >hg18.chr20(+):56827368-56827443|hg18_0
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131 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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132 >panTro2.chr20(+):56528685-56528760|panTro2_0
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133 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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134 >rheMac2.chr10(-):89144112-89144181|rheMac2_0
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135 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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136 >mm8.chr2(+):173910832-173910893|mm8_0
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137 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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138 >canFam2.chr24(+):46551822-46551889|canFam2_0
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139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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140
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141 >hg18.chr20(+):56827443-56827480|hg18_1
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142 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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143 >panTro2.chr20(+):56528760-56528797|panTro2_1
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144 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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145 >rheMac2.chr10(-):89144181-89144218|rheMac2_1
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146 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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147
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148 -----
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149
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150 **Example 2b**: Multiple Block Approach **Include hg18 and mm8** and **exclude blocks with missing species**:
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151
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152 The following alignment::
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153
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154 ##maf version=1
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155 a score=68686.000000
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156 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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157 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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158 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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159 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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160 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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161
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162 a score=10289.000000
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163 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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164 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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165 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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166
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167 will be converted to (**note** that the second MAF block, which does not have mm8, is not included in the output)::
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168
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169 >hg18.chr20(+):56827368-56827443|hg18_0
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170 GACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC
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171 >mm8.chr2(+):173910832-173910893|mm8_0
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172 AGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------
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173
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174 ------
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175
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176 .. class:: infomark
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177
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178 **About formats**
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179
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180 **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
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181
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182 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
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183 - Each sequence in an alignment is on a single line.
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184 - Lines starting with # are considered to be comments.
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185 - 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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186 - Some MAF files may contain two optional line types:
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187
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188 - 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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189 - An "e" line containing information about the size of the gap between the alignments that span the current block.
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190
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191 ------
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192
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193 **Citation**
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194
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195 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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196
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197
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198 </help>
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199 </tool>
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