Mercurial > repos > devteam > vcf2pgsnp
view vcf2pgSnp.xml @ 0:5fca46616675 draft default tip
Imported from capsule None
author | devteam |
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date | Mon, 28 Jul 2014 11:55:29 -0400 |
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<tool id="vcf2pgSnp" name="VCF to pgSnp" hidden="false" version="1.0.0"> <description>Convert from VCF to pgSnp format</description> <command interpreter="perl"> #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1 #else #vcf2pgSnp.pl $inType.ind_column $input1 > $out_file1 #end if </command> <inputs> <param format="vcf" name="input1" type="data" label="VCF dataset" /> <conditional name="inType"> <param name="how" type="select" label="How to treat individuals"> <option value="all">Group all as a population</option> <option value="one">Do just one individual</option> </param> <when value="one"> <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" /> </when> <when value="all"> <!-- do nothing --> </when> </conditional> </inputs> <outputs> <data format="interval" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" /> <param name="how" value="all" /> <output name="output" file="vcf2pgSnp_output.pgSnp" /> </test> </tests> <help> **Dataset formats** The input dataset is VCF_ format. The output dataset is pgSnp_. (`Dataset missing?`_) .. _Dataset missing?: ./static/formatHelp.html .. _VCF: ./static/formatHelp.html#vcf .. _pgSnp: ./static/formatHelp.html#pgSnp ----- **What it does** This converts a VCF dataset to pgSnp with the frequency counts being chromosome counts. If there is more than one column of SNP data it will either accumulate all columns as a population or convert the column indicated to pgSnp. ----- **Examples** - input:: 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48 etc. - output as a population:: chr1 13326 13327 G/C 2 7,1 0,0 chr1 13979 13980 T/C 2 7,1 0,0 chr1 30922 30923 G/T 2 4,4 0,0 etc. - output for each column separately:: chr1 13326 13327 G 1 2 0 G/C 2 1,1 0,0 G 1 2 0 G 1 2 0 chr1 13979 13980 T 1 2 0 T/C 2 1,1 0,0 T 1 2 0 T 1 2 0 chr1 30922 30923 T 1 2 0 G 1 2 0 G 1 2 0 T 1 2 0 etc. </help> </tool>