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comparison gd_snp2vcf.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
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30:4188853b940b 31:a631c2f6d913
1 <tool id="gd_gd_snp2vcf" name="gd_snp to VCF" version="1.1.0" force_history_refresh="True">
2 <description>: Convert from gd_snp or gd_genotype to VCF format, for submission to dbSNP</description>
3
4 <command interpreter="perl">
5 gd_snp2vcf.pl "$input" -handle=$hand -batch=$batch -ref=$ref -metaOut=$output2
6 #if $individuals.choice == '0':
7 #set $geno = ''
8 #for $individual_col in $input.dataset.metadata.individual_columns
9 ##need to check to number of cols per individual
10 #if $input.ext == "gd_snp":
11 #set $t = $individual_col + 2
12 #else if $input.ext == "gd_genotype":
13 #set $t = $individual_col
14 #else:
15 #set $t = $individual_col
16 #end if
17 #set $geno += "%d," % ($t)
18 #end for
19 #if $individuals.pall_id != '':
20 -population=$individuals.pall_id
21 #end if
22 #else if $individuals.choice == '1':
23 #set $geno = ''
24 #set $pop = ''
25 #if $input.ext == "gd_snp":
26 -off=2
27 #else if $input.ext == "gd_genotype":
28 -off=0
29 #else:
30 -off=2
31 #end if
32 #for $population in $individuals.populations
33 #set $geno += "%s," % ($population.p1_input)
34 #set $pop += "%s," % ($population.p1_id)
35 #end for
36 -population=$pop
37 #else if $individuals.choice == '2':
38 #set $geno = $individuals.geno
39 #end if
40 -geno=$geno
41 #if $bioproj.value != '':
42 -bioproj=$bioproj
43 #end if
44 #if $biosamp.value != '':
45 -biosamp=$biosamp
46 #end if
47 > $output
48 </command>
49
50 <inputs>
51 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
52 <conditional name="individuals">
53 <param name="choice" type="select" label="Generate dataset for">
54 <option value="0" selected="true">All individuals</option>
55 <option value="1">Individuals in populations</option>
56 <option value="2">A single individual</option>
57 </param>
58 <when value="0">
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" />
60 </when>
61 <when value="1">
62 <repeat name="populations" title="Population" min="1">
63 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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" />
65 </repeat>
66 </when>
67 <when value="2">
68 <param name="geno" type="data_column" data_ref="input" label="Column containing genotype" value="8" />
69 </when>
70 </conditional>
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" />
72 <param name="batch" type="text" size="20" label="Batch ID" help="ID used to tie dbSNP metadata to the VCF submission" />
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/)" />
74 <param name="bioproj" type="text" size="20" label="Optional: Registered BioProject ID" />
75 <param name="biosamp" type="text" size="20" label="Optional: Comma-separated list of registered BioSample IDs" />
76 </inputs>
77
78 <outputs>
79 <data name="output" format="vcf" />
80 <data name="output2" format="text" />
81 </outputs>
82
83 <tests>
84 <test>
85 <param name="input" value="sample.gd_snp" ftype="gd_snp" />
86 <param name="choice" value="2" />
87 <param name="geno" value="11" />
88 <param name="hand" value="MyHandle" />
89 <param name="batch" value="Test1" />
90 <param name="ref" value="pb_000001.1" />
91 <output name="output" file="snpsForSubmission.vcf" ftype="vcf" compare="diff" />
92 <output name="output2" file="snpsForSubmission.text" ftype="text" compare="diff" />
93 </test>
94 </tests>
95
96 <help>
97
98 **Dataset formats**
99
100 The input dataset is in gd_snp_ or gd_genotype_ format.
101 The output consists of two datasets needed for submitting SNPs:
102 a VCF_ file in the specific format required by dbSNP, and a partially
103 completed text_ file for the associated dbSNP metadata.
104 (`Dataset missing?`_)
105
106 .. _gd_snp: ./static/formatHelp.html#gd_snp
107 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
108 .. _VCF: ./static/formatHelp.html#vcf
109 .. _text: ./static/formatHelp.html#text
110 .. _Dataset missing?: ./static/formatHelp.html
111
112 -----
113
114 **What it does**
115
116 This tool converts a dataset in gd_snp or gd_genotype format to a VCF file formatted
117 for submission to the dbSNP database at NCBI. It also creates a partially
118 filled-in template to assist you in preparing the required "metadata" file
119 describing the SNP submission.
120
121 -----
122
123 **Example**
124
125 - input::
126
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",
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"}
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
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
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
132 etc.
133
134 - VCF output (for all individuals, and giving a population ID)::
135
136 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PB
137 Contig161 115 Contig161;115 C T 73.5 . VRT=6 NA:AC 8:0
138 Contig48 11 Contig48;11 A G 94.3 . VRT=6 NA:AC 8:0
139 Contig 66 Contig20;66 C T 54.0 . VRT=6 NA:AC 8:0
140 etc.
141
142 Note: This excerpt from the output does not show all of the headers. Also,
143 if the population ID had not been given, then the last two columns would not
144 appear in the output.
145
146 -----
147
148 **Reference**
149
150 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
151 dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001
152 Jan 1;29(1):308-11.
153
154 </help>
155 </tool>