Mercurial > repos > xuebing > sharplabtool
diff tools/maf/vcf_to_maf_customtrack.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/vcf_to_maf_customtrack.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,127 @@ +<tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track"> + <description>for display at UCSC</description> + <command interpreter="python">vcf_to_maf_customtrack.py '$out_file1' + #if $vcf_source_type.vcf_file + '${vcf_source_type.vcf_file[0].vcf_input.dbkey}' + #else + '?' + #end if + ${vcf_source_type.vcf_source} -n '$track_name' + #for $vcf_repeat in $vcf_source_type.vcf_file + '${vcf_repeat.vcf_input}' + #if $vcf_source_type.vcf_source == '-p' + '${vcf_repeat.population_name}' + #end if + #end for + -g + </command> + <inputs> + <param name="track_name" type="text" label="Custom Track Name" value="Galaxy Custom Track" size="30" /> + <conditional name="vcf_source_type"> + <param name="vcf_source" type="select" label="VCF Source Source Type"> + <option value="-p" selected="true">Per Population (file)</option> + <option value="-s">Per Sample</option> + </param> + <when value="-p"> + <repeat name="vcf_file" title="VCF population file" min="1"> + <param format="tabular" name="vcf_input" type="data" label="VCF file"/> + <param name="population_name" type="text" label="Name for this population" value=""/> + </repeat> + </when> + <when value="-s"> + <repeat name="vcf_file" title="VCF sample file" min="1"> + <param format="tabular" name="vcf_input" type="data" label="VCF file"/> + <!-- add column count validator >= 8? --> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data format="mafcustomtrack" name="out_file1" /> + </outputs> +<!-- <tests> + <test> + <param name="track_name" value="Galaxy Custom Track"/> + <param name="vcf_source" value="Per Population"/> + <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/> + <param name="population_name" value=""/> + <output name="out_file1" file="vcf_to_maf_population_out.mafcustomtrack"/> + </test> + <test> + <param name="track_name" value="Galaxy Custom Track"/> + <param name="vcf_source" value="Per Sample"/> + <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/> + <output name="out_file1" file="vcf_to_maf_sample_out.mafcustomtrack"/> + </test> + </tests> --> + <help> +**What it does** + +This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers. + +This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis. + +*Unknown nucleotides* are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence. + +**Example** + +Starting with a VCF:: + + ##fileformat=VCFv3.3 + ##fileDate=20090805 + ##source=myImputationProgramV3.1 + ##reference=1000GenomesPilot-NCBI36 + ##phasing=partial + ##INFO=NS,1,Integer,"Number of Samples With Data" + ##INFO=DP,1,Integer,"Total Depth" + ##INFO=AF,-1,Float,"Allele Frequency" + ##INFO=AA,1,String,"Ancestral Allele" + ##INFO=DB,0,Flag,"dbSNP membership, build 129" + ##INFO=H2,0,Flag,"HapMap2 membership" + ##FILTER=q10,"Quality below 10" + ##FILTER=s50,"Less than 50% of samples have data" + ##FORMAT=GT,1,String,"Genotype" + ##FORMAT=GQ,1,Integer,"Genotype Quality" + ##FORMAT=DP,1,Integer,"Read Depth" + ##FORMAT=HQ,2,Integer,"Haplotype Quality" + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 20 14370 rs6054257 G A 29 0 NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:-1,-1 + 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:-1,-1 + 20 1110696 rs6040355 A G,T 67 0 NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:-1,-1 + 20 1230237 . T . 47 0 NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2:-1,-1 + 20 1234567 microsat1 G D4,IGA 50 0 NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 + + + + +Under the following conditions: **VCF Source type:** *Per Population (file)*, **Name for this population:** *CHB+JPT* +Results in the following MAF custom track:: + + track name="Galaxy Custom Track" visibility=pack + ##maf version=1 + a score=0 + s hg18.chr20 14369 1 + 14370 G + s CHB+JPT_1.1 0 1 + 1 A + + a score=0 + s hg18.chr20 17329 1 + 17330 T + s CHB+JPT_1.2 0 1 + 1 A + + a score=0 + s hg18.chr20 1110695 1 + 1110696 A + s CHB+JPT_1.3 0 1 + 1 G + s CHB+JPT_2.3 0 1 + 1 T + + a score=0 + s hg18.chr20 1230236 1 + 1230237 T + s CHB+JPT_1.4 0 1 + 1 . + + a score=0 + s hg18.chr20 1234565 5 + 1234572 *G--*** + s CHB+JPT_1.5 0 1 + 1 *------ + s CHB+JPT_2.5 0 7 + 7 *GGA*** + + + </help> +</tool> +