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annotate gd_snp2vcf.xml @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents a631c2f6d913
children
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1 <tool id="gd_gd_snp2vcf" name="gd_snp to VCF" version="1.1.0" force_history_refresh="True">
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2 <description>: Convert from gd_snp or gd_genotype 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 #if $input.ext == "gd_snp":
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11 #set $t = $individual_col + 2
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12 #else if $input.ext == "gd_genotype":
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13 #set $t = $individual_col
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14 #else:
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15 #set $t = $individual_col
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16 #end if
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17 #set $geno += "%d," % ($t)
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18 #end for
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19 #if $individuals.pall_id != '':
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20 -population=$individuals.pall_id
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21 #end if
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22 #else if $individuals.choice == '1':
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23 #set $geno = ''
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24 #set $pop = ''
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25 #if $input.ext == "gd_snp":
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26 -off=2
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27 #else if $input.ext == "gd_genotype":
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28 -off=0
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29 #else:
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30 -off=2
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31 #end if
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32 #for $population in $individuals.populations
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33 #set $geno += "%s," % ($population.p1_input)
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34 #set $pop += "%s," % ($population.p1_id)
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35 #end for
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36 -population=$pop
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37 #else if $individuals.choice == '2':
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38 #set $geno = $individuals.geno
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39 #end if
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40 -geno=$geno
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41 #if $bioproj.value != '':
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42 -bioproj=$bioproj
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43 #end if
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44 #if $biosamp.value != '':
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45 -biosamp=$biosamp
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46 #end if
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47 > $output
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48 </command>
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49
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50 <inputs>
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51 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
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52 <conditional name="individuals">
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53 <param name="choice" type="select" label="Generate dataset for">
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54 <option value="0" selected="true">All individuals</option>
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55 <option value="1">Individuals in populations</option>
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56 <option value="2">A single individual</option>
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57 </param>
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58 <when value="0">
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59 <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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60 </when>
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61 <when value="1">
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62 <repeat name="populations" title="Population" min="1">
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63 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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64 <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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65 </repeat>
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66 </when>
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67 <when value="2">
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68 <param name="geno" type="data_column" data_ref="input" label="Column containing genotype" value="8" />
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69 </when>
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70 </conditional>
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71 <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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72 <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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73 <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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74 <param name="bioproj" type="text" size="20" label="Optional: Registered BioProject ID" />
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75 <param name="biosamp" type="text" size="20" label="Optional: Comma-separated list of registered BioSample IDs" />
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76 </inputs>
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77
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78 <outputs>
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79 <data name="output" format="vcf" />
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80 <data name="output2" format="text" />
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <param name="input" value="sample.gd_snp" ftype="gd_snp" />
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86 <param name="choice" value="2" />
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87 <param name="geno" value="11" />
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88 <param name="hand" value="MyHandle" />
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89 <param name="batch" value="Test1" />
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90 <param name="ref" value="pb_000001.1" />
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91 <output name="output" file="snpsForSubmission.vcf" ftype="vcf" compare="diff" />
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92 <output name="output2" file="snpsForSubmission.text" ftype="text" compare="diff" />
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93 </test>
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94 </tests>
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95
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96 <help>
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97
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98 **Dataset formats**
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99
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100 The input dataset is in gd_snp_ or gd_genotype_ format.
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101 The output consists of two datasets needed for submitting SNPs:
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102 a VCF_ file in the specific format required by dbSNP, and a partially
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103 completed text_ file for the associated dbSNP metadata.
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104 (`Dataset missing?`_)
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105
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106 .. _gd_snp: ./static/formatHelp.html#gd_snp
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107 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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108 .. _VCF: ./static/formatHelp.html#vcf
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109 .. _text: ./static/formatHelp.html#text
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110 .. _Dataset missing?: ./static/formatHelp.html
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111
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112 -----
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113
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114 **What it does**
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115
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116 This tool converts a dataset in gd_snp or gd_genotype format to a VCF file formatted
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117 for submission to the dbSNP database at NCBI. It also creates a partially
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118 filled-in template to assist you in preparing the required "metadata" file
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119 describing the SNP submission.
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120
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121 -----
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122
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123 **Example**
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124
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125 - input::
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126
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127 #{"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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128 #"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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129 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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130 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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131 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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132 etc.
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133
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134 - VCF output (for all individuals, and giving a population ID)::
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135
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136 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PB
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137 Contig161 115 Contig161;115 C T 73.5 . VRT=6 NA:AC 8:0
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138 Contig48 11 Contig48;11 A G 94.3 . VRT=6 NA:AC 8:0
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139 Contig 66 Contig20;66 C T 54.0 . VRT=6 NA:AC 8:0
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140 etc.
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141
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142 Note: This excerpt from the output does not show all of the headers. Also,
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143 if the population ID had not been given, then the last two columns would not
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144 appear in the output.
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145
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146 -----
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147
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148 **Reference**
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149
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150 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
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151 dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001
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152 Jan 1;29(1):308-11.
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153
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154 </help>
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155 </tool>