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comparison tools/evolution/codingSnps.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="hgv_codingSnps" name="aaChanges" version="1.0.0">
2 <description>amino-acid changes caused by a set of SNPs</description>
3
4 <command interpreter="perl">
5 codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 > $out_file1
6 </command>
7
8 <inputs>
9 <param format="interval" name="input1" type="data" label="SNP dataset">
10 <validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
11 </param>
12 <param name="col1" type="data_column" data_ref="input1" label="Column with SNPs" />
13 <param format="interval" name="input2" type="data" label="Gene dataset">
14 <validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
15 </param>
16 </inputs>
17
18 <outputs>
19 <data format="tabular" name="out_file1" />
20 </outputs>
21
22 <code file="codingSnps_filter.py"></code>
23
24 <requirements>
25 <requirement type="binary">cat</requirement>
26 <requirement type="binary">sort</requirement>
27 <requirement type="package">ucsc_tools</requirement>
28 </requirements>
29
30 <tests>
31 <test>
32 <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" />
33 <param name="col1" value="6" />
34 <param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" />
35 <output name="output" file="codingSnps_output1.interval" />
36 </test>
37 <test>
38 <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
39 <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
40 <param name="col1" value="4" />
41 <output name="output" file="codingSnps_output2.interval" />
42 </test>
43 </tests>
44
45 <help>
46 .. class:: infomark
47
48 The build must be defined for the input files and must be the same for both files.
49 Use the pencil icon to add the build to the files if necessary.
50
51 -----
52
53 **Dataset formats**
54
55 The SNP dataset is in interval_ format, with a column of SNPs as described below.
56 The gene dataset is in BED_ format with 12 columns. The output dataset is also interval.
57 (`Dataset missing?`_)
58
59 .. _interval: ./static/formatHelp.html#interval
60 .. _BED: ./static/formatHelp.html#bed
61 .. _Dataset missing?: ./static/formatHelp.html
62
63 -----
64
65 **What it does**
66
67 This tool identifies which SNPs create amino-acid changes in the specified
68 coding regions. The first input file contains the SNPs and must be an interval file.
69 It needs the chromosome, start, and end position as well as the SNP. The
70 SNP can be given using ambiguous-nucleotide symbols or a list of two to four
71 alleles
72 separated by '/'. Any other columns in the first input file will not be
73 used but will be kept for the output. The second input file contains the genes
74 to be used for defining the coding regions. This file must be a BED file with
75 the first 12 columns standard BED columns. The output is the same as the
76 first input file with
77 several columns added: the name field from the line of the gene input file
78 used, the amino acids, the codon number, and the reference nucleotide that
79 changed in the amino acid.
80 The amino acids are listed with the reference amino acid first, then a colon,
81 and then the amino acids for the alleles. If a SNP is not in a coding region
82 or is synonymous then it is not included in the output file.
83
84 -----
85
86 **Example**
87
88 - first input file, with SNPs::
89
90 chr22 15660821 15660822 A/G
91 chr22 15825725 15825726 G/T
92 chr22 15827035 15827036 G
93 chr22 15827135 15827136 C/G
94 chr22 15830928 15830929 A/G
95 chr22 15830951 15830952 G
96 chr22 15830955 15830956 C/T
97 chr22 15848885 15848886 C/T
98 chr22 15849048 15849049 A/C
99 chr22 15919711 15919712 A/G
100 etc.
101
102 or, indicating polymorphisms using ambiguous-nucleotide symbols::
103
104 chr22 15660821 15660822 R
105 chr22 15825725 15825726 K
106 chr22 15827035 15827036 G
107 chr22 15827135 15827136 S
108 chr22 15830928 15830929 R
109 chr22 15830951 15830952 G
110 chr22 15830955 15830956 Y
111 chr22 15848885 15848886 Y
112 chr22 15849048 15849049 M
113 chr22 15919711 15919712 R
114 etc.
115
116 - second input file, with UCSC annotations for human genes::
117
118 chr22 15688363 15690225 uc010gqr.1 0 + 15688363 15688363 0 2 587,794, 0,1068,
119 chr22 15822826 15869112 uc002zlw.1 0 - 15823622 15869004 0 10 940,105,97,91,265,86,251,208,304,282, 0,1788,2829,3241,4163,6361,8006,26023,29936,46004,
120 chr22 15826991 15869112 uc010gqs.1 0 - 15829218 15869004 0 5 1380,86,157,304,282, 0,2196,21858,25771,41839,
121 chr22 15897459 15919682 uc002zlx.1 0 + 15897459 15897459 0 4 775,128,103,1720, 0,8303,10754,20503,
122 chr22 15945848 15971389 uc002zly.1 0 + 15945981 15970710 0 13 271,25,147,113,127,48,164,84,85,12,102,42,2193, 0,12103,12838,13816,15396,17037,17180,18535,19767,20632,20894,22768,23348,
123 etc.
124
125 - output file, showing non-synonymous substitutions in coding regions::
126
127 chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 T
128 chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 C
129 chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 C
130 chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 C
131 chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 A
132 chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 T
133 chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 G
134 chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 G
135 chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 C
136 etc.
137
138 </help>
139 </tool>