Mercurial > repos > miller-lab > genome_diversity
view multiple_to_gd_genotype.xml @ 28:184d14e4270d
Update to Miller Lab devshed revision 4ede22dd5500
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 17 Jul 2013 12:46:46 -0400 |
| parents | 8997f2ca8c7a |
| children |
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<tool id="gd_multiple_to_gd_genotype" name="Convert" version="1.0.0"> <description>: CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype</description> <command interpreter="python"> #import base64 #set species_arg = base64.b64encode(str($species)) multiple_to_gd_genotype.py --input '$input' --output '$output' --dbkey '$dbkey' --species '$species_arg' --format '$input_format' </command> <inputs> <param name="input" type="data" format="txt" label="Input dataset" /> <param name="input_format" type="select" label="Input format"> <option value="csv" selected="true">CSV</option> <option value="fstat">FSTAT</option> <option value="genepop">Genepop</option> <option value="vcf">VCF</option> </param> <param name="species" type="text" label="Focus species"> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <param name="dbkey" type="genomebuild" label="Reference species" /> </inputs> <outputs> <data name="output" format="gd_genotype" /> </outputs> <!-- <tests> <test> <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> <param name="lo_coverage" value="0" /> <param name="hi_coverage" value="1000" /> <param name="low_ind_cov" value="3" /> <param name="lo_quality" value="30" /> <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> </test> </tests> --> <help> **Dataset formats** The input dataset is formated as VCF, FSTAT, Genepop, or CSV, and is of Galaxy datatype text_. Additionally, the name of the focus species (from which the SNPs in the VCF file were obtained) and a reference species are required. The output dataset is in gd_genotype_ or gd_snp_ format. For input datasets in Genepop, FSTAT, or CSV formats, the program ignores population structures as well as alleles other than those encoded by 0, 1, and 2. For input datasets in FSTAT format the program accepts up to 9 digits and for Genepop files only 2 digits. Chromosome and position for each SNPs must be separated by a space or a tab. Ancestral loci must be encoded as 1, derived as 2 and missing as 0. In all cases ancestral and derived SNPs are returned as N. Alternatively, a dataset in CSV format can include nucleotides. In this case the ancestral nucleotide is defined as the most common allele. .. _text: ./static/formatHelp.html#text .. _gd_snp: ./static/formatHelp.html#gd_snp .. _gd_genotype: ./static/formatHelp.html#gd_genotype ----- **What it does** This tool returns a gd_genotype dataset from VCF formatted files or three other conventional population genetics formats (i.e. FSTAT, Genepop, and CSV). For VCF files that include the fields allelic depth, genotype quality and genotype ("AD", "GQ", and "GT" respectively in the "FORMAT" field) the input dataset can be converted into a gd_snp file. ----- **Examples** - If the input format is VCF and includes the fields allelic depth, genotype quality and genotype ("AD", "GQ", and "GT" respectively in the "FORMAT" field). Focus species name is "aye-aye" and reference species is "Human Feb. 2009 (GRCh37/hg19) (hg19)":: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 19_F 19.1_F 19.2_F Chr21 382242 rs134033430 T C 3296.97 . . GT:GQ:DP:PL:AD 1/1:75:26:943,75,0:0,26 1/1:3:1:30,3,0:0,1 ./. Chr21 383680 rs137652597 T C 2236.62 . . GT:GQ:DP:PL:AD 1/1:36:12:436,36,0:0,12 ./. 1/1:3:1:31,3,0:0,1 Chr21 387251 . G T 2407.88 . . GT:GQ:DP:PL:AD 1/1:30:12:394,30,0:0,10 ./. ./. etc. - output (gd_snp):: #{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q"],"dbkey":"aye-aye","individuals":[["19_F",6],["19.1_F",10],["19.2_F",14]],"pos":2,"rPos":2,"ref":1, #"scaffold":1,"species":"hg19"} Chr21 382242 T C 3296.97 0 26 0 75 0 1 0 3 0 0 -1 -1 Chr21 383680 T C 2236.62 0 12 0 36 0 0 -1 -1 0 1 0 3 Chr21 387251 G T 2407.88 0 10 0 30 0 0 -1 -1 0 0 -1 -1 etc. - If the input format is VCF, focus species is "aye-aye" and reference species is "Human Feb. 2009 (GRCh37/hg19) (hg19)":: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 19_F 19.1_F 19.2_F Chr21 382242 rs134033430 T C 3296.97 . . GT:GQ:DP:PL 1/1:75:26:943,75,0 1/1:3:1:30,3,0:0,1 ./. Chr21 383680 rs137652597 T C 2236.62 . . GT:GQ:DP:PL 1/1:36:12:436,36,0 ./. 1/1:3:1:31,3,0:0,1 Chr21 387251 . G T 2407.88 . . GT:GQ:DP:PL 1/1:30:12:394,30,0 ./. ./. etc. - output (gd_genotype):: #{"column_names":["chr","pos","A","B","1G","2G","3G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} Chr21 382242 T C 0 0 -1 Chr21 383680 T C 0 -1 0 Chr21 387251 G T 0 -1 -1 etc. - If the input format is Genepop:: Microsat on aye-aye from different locations Chr21 382242, Chr21 383680, Chr21 387251 POP 19_F, 0202 0202 0202 Pop 19.1_F, 0202 0000 0000 19.2_F, 0000 0202 0000 etc. - or the input format is FSTAT:: 300 3 2 1 Chr21 382242 Chr21 383680 Chr21 387251 19_F 22 22 22 19.1_F 22 00 00 19.2_F 00 22 00 etc. - or the input format is CSV:: ,19_F,19.1_F,19.2_F,... Chr21 382242,22,22,00 Chr21 383680,22,00,22 Chr21 387251,22,00,00 etc. - output (gd_genotype):: #{"column_names":["chr","pos","A","B","1G","2G","3G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} Chr21 382242 N N 0 0 -1 Chr21 383680 N N 0 -1 0 Chr21 387251 N N 0 -1 -1 etc. - if the input format is CSV:: ,19_F,19.1_F,19.2_F,... Chr21 382242,C,C,N Chr21 383680,C,N,C Chr21 387251,T,N,N etc. - output (gd_genotype):: #{"column_names":["chr","pos","A","B","1G","2G","3G","4G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7],["...",8]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} Chr21 382242 C N 2 2 -1 Chr21 383680 T N 2 -1 2 Chr21 387251 T N 2 -1 -1 etc. </help> </tool>