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comparison tools/maf/maf_to_bed.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="MAF_To_BED1" name="Maf to BED" force_history_refresh="True">
2 <description>Converts a MAF formatted file to the BED format</description>
3 <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks $__new_file_path__</command>
4 <inputs>
5 <param format="maf" name="input1" type="data" label="MAF file to convert"/>
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">
7 <options>
8 <filter type="data_meta" ref="input1" key="species" />
9 </options>
10 </param>
11 <param name="complete_blocks" type="select" label="Exclude blocks which have a requested species missing">
12 <option value="partial_allowed">include blocks with missing species</option>
13 <option value="partial_disallowed">exclude blocks with missing species</option>
14 </param>
15 </inputs>
16 <outputs>
17 <data format="bed" name="out_file1" />
18 </outputs>
19 <tests>
20 <test>
21 <param name="input1" value="4.maf"/>
22 <param name="species" value="hg17"/>
23 <param name="complete_blocks" value="partial_disallowed"/>
24 <output name="out_file1" file="cf_maf_to_bed.dat"/>
25 </test>
26 </tests>
27 <help>
28
29 **What it does**
30
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.
32
33 The interface for this tool contains two pages (steps):
34
35 * **Step 1 of 2**. Choose multiple alignments from history to be converted to BED format.
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:
37
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.
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).
40
41
42 -----
43
44 **Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
45
46 For the following alignment::
47
48 ##maf version=1
49 a score=68686.000000
50 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
51 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
52 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
53 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
54 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
55
56 a score=10289.000000
57 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
58 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
59 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
60
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.)::
62
63 chr20 56827368 56827443 hg18_0 0 +
64 chr20 56827443 56827480 hg18_1 0 +
65
66 -----
67
68 **Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
69
70 For the following alignment::
71
72 ##maf version=1
73 a score=68686.000000
74 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
75 s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
76 s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
77 s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
78 s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
79
80 a score=10289.000000
81 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
82 s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
83 s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
84
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):
86
87 History item **1** (for hg18)::
88
89 chr20 56827368 56827443 hg18_0 0 +
90
91 History item **2** (for mm8)::
92
93 chr2 173910832 173910893 mm8_0 0 +
94
95 -------
96
97 .. class:: infomark
98
99 **About formats**
100
101 **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
102
103 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
104 - Each sequence in an alignment is on a single line.
105 - Lines starting with # are considered to be comments.
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.
107 - Some MAF files may contain two optional line types:
108
109 - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
110 - An "e" line containing information about the size of the gap between the alignments that span the current block.
111
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:
113
114 The first three BED fields (required) are::
115
116 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
117 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
118 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
119
120 Additional (optional) fields are::
121
122 4. name - The name of the BED line.
123 5. score - A score between 0 and 1000.
124 6. strand - Defines the strand - either '+' or '-'.
125
126 ------
127
128 **Citation**
129
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
131
132
133 </help>
134 <code file="maf_to_bed_code.py"/>
135 </tool>
136