root/galaxy-central/tools/maf/maf_to_interval.xml @ 3

リビジョン 2, 8.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True">
2  <description>Converts a MAF formatted file to the Interval format</description>
3  <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command>
4  <inputs>
5    <param format="maf" name="input1" type="data" label="MAF file to convert"/>
6    <param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species.">
7      <options>
8        <filter type="data_meta" ref="input1" key="species" />
9        <filter type="remove_value" meta_ref="input1" key="dbkey" />
10      </options>
11    </param>
12    <param name="complete_blocks" type="select" label="Exclude blocks which have a species missing">
13      <option value="partial_allowed">include blocks with missing species</option>
14      <option value="partial_disallowed">exclude blocks with missing species</option>
15    </param>
16    <param name="remove_gaps" type="select" label="Remove Gap characters from sequences">
17      <option value="keep_gaps">keep gaps</option>
18      <option value="remove_gaps">remove gaps</option>
19    </param>
20  </inputs>
21  <outputs>
22    <data format="interval" name="out_file1" />
23  </outputs>
24  <tests>
25    <test>
26      <param name="input1" value="4.maf" dbkey="hg17"/>
27      <param name="complete_blocks" value="partial_disallowed"/>
28      <param name="remove_gaps" value="keep_gaps"/>
29      <param name="species" value="panTro1" />
30      <output name="out_file1" file="maf_to_interval_out_hg17.interval"/>
31      <output name="out_file1" file="maf_to_interval_out_panTro1.interval"/>
32    </test>
33  </tests>
34  <help>
35
36**What it does**
37
38This tool converts every MAF block to a set of genomic intervals describing the position of that alignment block within a corresponding genome. Sequences from aligning species are also included in the output.
39
40The interface for this tool contains several options:
41
42 * **MAF file to convert**. Choose multiple alignments from history to be converted to BED format.
43 * **Choose species**. Choose additional species from the alignment to be included in the output
44 * **Exclude blocks which have a species missing**. if an alignment block does not contain any one of the species found in the alignment set 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).
45 * **Remove Gap characters from sequences**. Gaps can be removed from sequences before they are output.
46
47
48-----
49
50**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
51
52For the following alignment::
53
54  ##maf version=1
55  a score=68686.000000
56  s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
57  s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
58  s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
59  s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
60  s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
61
62  a score=10289.000000
63  s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
64  s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
65  s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
66
67the tool will create **a single** history item containing the following (**note** the name field is numbered iteratively: hg18_0_0, hg18_1_0 etc. where the first number is the block number and the second number is the iteration through the block (if a species appears twice in a block, that interval will be repeated) and sequences for each species are included in the order specified in the header: the field is left empty when no sequence is available for that species)::
68
69  #chrom        start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2
70  chr20 56827368        56827443        +       68686.0 hg18_0_0        CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
71  chr20 56827443        56827480        +       10289.0 hg18_1_0                ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG           ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG   ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
72
73
74-----
75
76**Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
77
78For the following alignment::
79
80  ##maf version=1
81  a score=68686.000000
82  s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
83  s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
84  s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
85  s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
86  s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
87
88  a score=10289.000000
89  s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
90  s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
91  s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
92
93the tool will create **two** history items (one for hg18 and one for 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):
94
95History item **1** (for hg18)::
96
97   #chrom       start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2
98   chr20        56827368        56827443        +       68686.0 hg18_0_0        CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
99
100
101History item **2** (for mm8)::
102
103   #chrom       start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2
104   chr2 173910832       173910893       +       68686.0 mm8_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
105
106
107-------
108
109.. class:: infomark
110
111**About formats**
112
113**MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
114
115 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
116 - Each sequence in an alignment is on a single line.
117 - Lines starting with # are considered to be comments.
118 - 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.
119 - Some MAF files may contain two optional line types:
120
121   - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
122   - An "e" line containing information about the size of the gap between the alignments that span the current block.
123
124
125    </help>
126</tool>
127
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。