/tools/maf/maf_to_fasta.xml
XML | 199 lines | 156 code | 43 blank | 0 comment | 0 complexity | 6070ce5f2311016787b776b577d7eff0 MD5 | raw file
1<tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1"> 2 <description>Converts a MAF formatted file to FASTA format</description> 3 <command interpreter="python"> 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 5 #else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1 6 #end if# 7 </command> 8 <inputs> 9 <param format="maf" name="input1" type="data" label="MAF file to convert"/> 10 <conditional name="fasta_target_type"> 11 <param name="fasta_type" type="select" label="Type of FASTA Output"> 12 <option value="multiple" selected="true">Multiple Blocks</option> 13 <option value="concatenated">One Sequence per Species</option> 14 </param> 15 <when value="multiple"> 16 <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="checked taxa will be included in the output"> 17 <options> 18 <filter type="data_meta" ref="input1" key="species" /> 19 </options> 20 </param> 21 <param name="complete_blocks" type="select" label="Choose to"> 22 <option value="partial_allowed">include blocks with missing species</option> 23 <option value="partial_disallowed">exclude blocks with missing species</option> 24 </param> 25 </when> 26 <when value="concatenated"> 27 <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true"> 28 <options> 29 <filter type="data_meta" ref="input1" key="species" /> 30 </options> 31 </param> 32 </when> 33 </conditional> 34 </inputs> 35 <outputs> 36 <data format="fasta" name="out_file1" /> 37 </outputs> 38 <tests> 39 <test> 40 <param name="input1" value="3.maf" ftype="maf"/> 41 <param name="fasta_type" value="concatenated"/> 42 <param name="species" value="canFam1"/> 43 <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/> 44 </test> 45 <test> 46 <param name="input1" value="4.maf" ftype="maf"/> 47 <param name="fasta_type" value="multiple"/> 48 <param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/> 49 <param name="complete_blocks" value="partial_allowed"/> 50 <output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/> 51 </test> 52 </tests> 53 <help> 54 55**Types of MAF to FASTA conversion** 56 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. 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. 59 60------- 61 62**What it does** 63 64This tool converts MAF blocks to FASTA format and concatenates them into a single FASTA block or outputs multiple FASTA blocks separated by empty lines. 65 66The interface for this tool contains two pages (steps): 67 68 * **Step 1 of 2**. Choose multiple alignments from history to be converted to FASTA format. 69 * **Step 2 of 2**. Choose the type of output as well as the species from the alignment to be included in the output. 70 71 Multiple Block output has additional options: 72 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). 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. 75 76 77----- 78 79**Example 1**: 80 81In the concatenated approach, the following alignment:: 82 83 ##maf version=1 84 a score=68686.000000 85 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 86 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 87 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 88 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 89 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 90 91 a score=10289.000000 92 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 93 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 94 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 95 96will be converted to (**note** that because mm8 (mouse) and canFam2 (dog) are absent from the second block, they are replaced with gaps after concatenation):: 97 98 >canFam2 99 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C------------------------------------- 100 >hg18 101 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 102 >mm8 103 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------------------------------------------- 104 >panTro2 105 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 106 >rheMac2 107 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 108 109------ 110 111**Example 2a**: Multiple Block Approach **Include all species** and **include blocks with missing species**: 112 113The following alignment:: 114 115 ##maf version=1 116 a score=68686.000000 117 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 118 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 119 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 120 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 121 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 122 123 a score=10289.000000 124 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 125 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 126 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 127 128will be converted to:: 129 130 >hg18.chr20(+):56827368-56827443|hg18_0 131 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 132 >panTro2.chr20(+):56528685-56528760|panTro2_0 133 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 134 >rheMac2.chr10(-):89144112-89144181|rheMac2_0 135 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 136 >mm8.chr2(+):173910832-173910893|mm8_0 137 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 138 >canFam2.chr24(+):46551822-46551889|canFam2_0 139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 140 141 >hg18.chr20(+):56827443-56827480|hg18_1 142 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 143 >panTro2.chr20(+):56528760-56528797|panTro2_1 144 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 145 >rheMac2.chr10(-):89144181-89144218|rheMac2_1 146 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 147 148----- 149 150**Example 2b**: Multiple Block Approach **Include hg18 and mm8** and **exclude blocks with missing species**: 151 152The following alignment:: 153 154 ##maf version=1 155 a score=68686.000000 156 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 157 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 158 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 159 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 160 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 161 162 a score=10289.000000 163 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 164 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 165 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 166 167will be converted to (**note** that the second MAF block, which does not have mm8, is not included in the output):: 168 169 >hg18.chr20(+):56827368-56827443|hg18_0 170 GACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC 171 >mm8.chr2(+):173910832-173910893|mm8_0 172 AGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------ 173 174------ 175 176.. class:: infomark 177 178**About formats** 179 180 **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes. 181 182 - The .maf format is line-oriented. Each multiple alignment ends with a blank line. 183 - Each sequence in an alignment is on a single line. 184 - Lines starting with # are considered to be comments. 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. 186 - Some MAF files may contain two optional line types: 187 188 - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; 189 - An "e" line containing information about the size of the gap between the alignments that span the current block. 190 191------ 192 193**Citation** 194 195If 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>`_ 196 197 198 </help> 199</tool>