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130 lines
7.0 KiB
XML
130 lines
7.0 KiB
XML
<tool id="MAF_To_BED1" name="MAF to BED" version="1.0.0" profile="16.04">
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<description>Converts a MAF formatted file to the BED format</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<code file="maf_to_bed_code.py"/>
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<command>python '$__tool_directory__/maf_to_bed.py' '${input1}' '${out_file1}' '${species}' ${complete_blocks} '.' '${out_file1.id}'</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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<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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<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="Exclude blocks which have a requested species missing">
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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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</inputs>
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<outputs>
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<data format="bed" 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="4.maf" ftype="maf"/>
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<param name="species" value="hg17"/>
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<param name="complete_blocks" value="partial_disallowed"/>
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<output name="out_file1" file="cf_maf_to_bed.dat"/>
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</test>
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</tests>
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<help>
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**What it does**
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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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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 BED format.
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* **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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* **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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* **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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-----
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**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
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For 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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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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chr20 56827368 56827443 hg18_0 0 +
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chr20 56827443 56827480 hg18_1 0 +
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-----
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**Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
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For 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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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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History item **1** (for hg18)::
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chr20 56827368 56827443 hg18_0 0 +
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History item **2** (for mm8)::
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chr2 173910832 173910893 mm8_0 0 +
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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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**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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The first three BED fields (required) are::
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1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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Additional (optional) fields are::
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4. name - The name of the BED line.
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5. score - A score between 0 and 1000.
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6. strand - Defines the strand - either '+' or '-'.
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</help>
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<expand macro="citations" />
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</tool>
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