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