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197 lines
10 KiB
XML
197 lines
10 KiB
XML
<tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1">
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<description>Converts a MAF formatted file to FASTA format</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<command>
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python
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#if $fasta_target_type.fasta_type == "multiple"
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'$__tool_directory__/maf_to_fasta_multiple_sets.py' '$input1' '$out_file1' $fasta_target_type.species $fasta_target_type.complete_blocks
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#else
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'$__tool_directory__/maf_to_fasta_concat.py' $fasta_target_type.species '$input1' '$out_file1'
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#end if
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</command>
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<inputs>
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<param format="maf" name="input1" type="data" label="MAF file to convert"/>
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<conditional name="fasta_target_type">
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<param name="fasta_type" type="select" label="Type of FASTA Output">
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<option value="multiple" selected="true">Multiple Blocks</option>
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<option value="concatenated">One Sequence per Species</option>
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</param>
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<when value="multiple">
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<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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<options>
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<filter type="data_meta" ref="input1" key="species" />
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</options>
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</param>
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<param name="complete_blocks" type="select" label="Choose to">
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<option value="partial_allowed">include blocks with missing species</option>
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<option value="partial_disallowed">exclude blocks with missing species</option>
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</param>
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</when>
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<when value="concatenated">
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<param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true">
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<options>
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<filter type="data_meta" ref="input1" key="species" />
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</options>
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</param>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="3.maf" ftype="maf"/>
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<param name="fasta_type" value="concatenated"/>
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<param name="species" value="canFam1"/>
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<output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>
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</test>
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<test>
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<param name="input1" value="4.maf" ftype="maf"/>
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<param name="fasta_type" value="multiple"/>
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<param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/>
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<param name="complete_blocks" value="partial_allowed"/>
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<output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/>
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</test>
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</tests>
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<help>
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**Types of MAF to FASTA conversion**
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* **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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* **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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-------
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**What it does**
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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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The interface for this tool contains two pages (steps):
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* **Step 1 of 2**. Choose multiple alignments from history to be converted to FASTA format.
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* **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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Multiple Block output has additional options:
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* **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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* **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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-----
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**Example 1**:
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In the concatenated approach, the following alignment::
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##maf version=1
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a score=68686.000000
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s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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a score=10289.000000
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s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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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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>canFam2
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CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C-------------------------------------
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>hg18
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GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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>mm8
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AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC--------------------------------------------
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>panTro2
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GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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>rheMac2
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GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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------
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**Example 2a**: Multiple Block Approach **Include all species** and **include blocks with missing species**:
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The following alignment::
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##maf version=1
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a score=68686.000000
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s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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a score=10289.000000
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s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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will be converted to::
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>hg18.chr20(+):56827368-56827443|hg18_0
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GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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>panTro2.chr20(+):56528685-56528760|panTro2_0
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GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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>rheMac2.chr10(-):89144112-89144181|rheMac2_0
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GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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>mm8.chr2(+):173910832-173910893|mm8_0
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AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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>canFam2.chr24(+):46551822-46551889|canFam2_0
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CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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>hg18.chr20(+):56827443-56827480|hg18_1
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ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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>panTro2.chr20(+):56528760-56528797|panTro2_1
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ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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>rheMac2.chr10(-):89144181-89144218|rheMac2_1
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ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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-----
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**Example 2b**: Multiple Block Approach **Include hg18 and mm8** and **exclude blocks with missing species**:
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The following alignment::
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##maf version=1
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a score=68686.000000
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s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
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s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
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s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
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s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
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a score=10289.000000
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s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
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s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
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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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>hg18.chr20(+):56827368-56827443|hg18_0
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GACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC
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>mm8.chr2(+):173910832-173910893|mm8_0
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AGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------
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------
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.. class:: infomark
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**About formats**
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**MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
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- The .maf format is line-oriented. Each multiple alignment ends with a blank line.
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- Each sequence in an alignment is on a single line.
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- Lines starting with # are considered to be comments.
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- 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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- Some MAF files may contain two optional line types:
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- 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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- An "e" line containing information about the size of the gap between the alignments that span the current block.
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</help>
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<expand macro="citations" />
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</tool>
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