Mercurial > repos > miller-lab > snp_analysis_conversion

annotate gd_snp2vcf.xml @ 3:edf12470a1a6 default tip

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Bugfix from Belinda, in vcf2pgSnp.pl
author Cathy Riemer <cathy+hg@bx.psu.edu>
date Thu, 19 Mar 2015 12:06:34 -0400
parents 35c20b109be5
children
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1 <tool id="gd_snp2vcf" name="gd_snp to VCF" version="1.0.0" force_history_refresh="True">
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2 <description>: Convert from gd_snp to VCF format, for submission to dbSNP</description>
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3
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4 <command interpreter="perl">
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5 gd_snp2vcf.pl "$input" -handle=$hand -batch=$batch -ref=$ref -metaOut=$output2
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6 #if $individuals.choice == '0'
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7 #set $geno = ''
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8 #for $individual_col in $input.dataset.metadata.individual_columns
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9 ##need to check to number of cols per individual
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10 #set $t = $individual_col + 2
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11 #set $geno += "%d," % ($t)
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12 #end for
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13 #if $individuals.pall_id != ''
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14 -population=$individuals.pall_id
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15 #end if
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16 #else if $individuals.choice == '1'
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17 #set $geno = ''
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18 #set $pop = ''
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19 #for $population in $individuals.populations
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20 -geno=`perl -ane 'print \$F[0]+2, ",";' $population.p1_input`
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21 #set $pop += "%s," % ($population.p1_id)
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22 #end for
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23 -population=$pop
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24 #else if $individuals.choice == '2'
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25 #set $geno = $individuals.geno
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26 #end if
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27 -geno=$geno
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28 #if $bioproj.value != ''
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29 -bioproj=$bioproj
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30 #end if
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31 #if $biosamp.value != ''
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32 -biosamp=$biosamp
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33 #end if
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34 > $output
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35 </command>
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36
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37 <inputs>
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38 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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39 <conditional name="individuals">
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40 <param name="choice" type="select" label="Generate dataset for">
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41 <option value="0" selected="true">All individuals</option>
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42 <option value="1">Individuals in populations</option>
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43 <option value="2">A single individual</option>
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44 </param>
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45 <when value="0">
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46 <param name="pall_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" />
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47 </when>
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48 <when value="1">
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49 <repeat name="populations" title="Population" min="1">
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50 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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51 <param name="p1_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" />
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52 </repeat>
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53 </when>
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54 <when value="2">
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55 <param name="geno" type="data_column" data_ref="input" label="Column containing genotype" value="8" />
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56 </when>
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57 </conditional>
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58 <param name="hand" type="text" size="20" label="dbSNP handle" help="If you do not have a handle, request one at http://www.ncbi.nlm.nih.gov/projects/SNP/handle.html" />
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59 <param name="batch" type="text" size="20" label="Batch ID" help="ID used to tie dbSNP metadata to the VCF submission" />
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60 <param name="ref" type="text" size="20" label="Reference sequence ID" help="The RefSeq assembly accession.version on which the SNP positions are based (see http://www.ncbi.nlm.nih.gov/assembly/)" />
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61 <param name="bioproj" type="text" size="20" label="Optional: Registered BioProject ID" />
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62 <param name="biosamp" type="text" size="20" label="Optional: Comma-separated list of registered BioSample IDs" />
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63 </inputs>
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64
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65 <outputs>
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66 <data name="output" format="vcf" />
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67 <data name="output2" format="text" />
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68 </outputs>
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69
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70 <tests>
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71 <test>
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72 <param name="input" value="sample.gd_snp" ftype="gd_snp" />
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73 <param name="choice" value="2" />
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74 <param name="geno" value="11" />
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75 <param name="hand" value="MyHandle" />
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76 <param name="batch" value="Test1" />
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77 <param name="ref" value="pb_000001.1" />
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78 <output name="output" file="snpsForSubmission.vcf" ftype="vcf" compare="diff" />
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79 <output name="output2" file="snpsForSubmission.text" ftype="text" compare="diff" />
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80 </test>
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81 </tests>
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82
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83 <help>
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84
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85 **Dataset formats**
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86
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87 The input dataset is in gd_snp_ format.
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88 The output consists of two datasets needed for submitting SNPs:
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89 a VCF_ file in the specific format required by dbSNP, and a partially
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90 completed text_ file for the associated dbSNP metadata.
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91 (`Dataset missing?`_)
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92
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93 .. _gd_snp: ./static/formatHelp.html#gd_snp
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94 .. _VCF: ./static/formatHelp.html#vcf
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95 .. _text: ./static/formatHelp.html#text
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96 .. _Dataset missing?: ./static/formatHelp.html
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97
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98 -----
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99
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100 **What it does**
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101
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102 This tool converts a dataset in gd_snp format to a VCF file formatted
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103 for submission to the dbSNP database at NCBI. It also creates a partially
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104 filled-in template to assist you in preparing the required "metadata" file
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105 describing the SNP submission.
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106
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107 -----
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108
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109 **Example**
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110
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111 - input::
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112
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113 #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
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114 #"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
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115 Contig161 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
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116 Contig48 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
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117 Contig20 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
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118 etc.
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119
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120 - VCF output (for all individuals, and giving a population ID)::
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121
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122 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PB
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123 Contig161 115 Contig161;115 C T 73.5 . VRT=6 NA:AC 8:0
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124 Contig48 11 Contig48;11 A G 94.3 . VRT=6 NA:AC 8:0
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125 Contig 66 Contig20;66 C T 54.0 . VRT=6 NA:AC 8:0
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126 etc.
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127
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128 Note: This excerpt from the output does not show all of the headers. Also,
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129 if the population ID had not been given, then the last two columns would not
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130 appear in the output.
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131
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132 -----
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133
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134 **Reference**
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135
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136 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
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137 dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001
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138 Jan 1;29(1):308-11.
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139
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140 </help>
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141 </tool>