Mercurial > repos > dereeper > sniplay3
view filterVCFonAnnotations.xml @ 2:15319113c0a5 draft
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author | dereeper |
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date | Thu, 12 Feb 2015 15:54:24 -0500 |
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<tool id="sniplay_filterVCFonAnnotations" name="Filter VCF on Annotations" version="1.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> </requirements> <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> <!-- tool_binary -v --> </version_command> <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> FilterVCFonAnnotations.pl --input $filein --out $fileout #if str( $genelist ) != "None": --genelist $genelist #end if #if str( $feature ) != "": --feature $feature #end if #if str( $syn ) != "": --syn $syn #end if </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> <param name="genelist" type="data" format="txt" optional="true" label="Genelist" default="" help="File listing the genes to be filtered, one line per individu/gene"/> <param name="feature" type="select" label="Genomic feature" optional="true" help="Filter within genomic feature"> <option value="" selected="true">All</option> <option value="Exon">Exon</option> <option value="INTRON">Intron</option> <option value="UTR_5_PRIME">UTR5prime</option> <option value="UTR_3_PRIME">UTR3prime</option> <option value="DOWNSTREAM">Downstream</option> <option value="UPSTREAM">Upstream</option> <option value="INTERGENIC">Intergenic</option> </param> <param name="syn" type="select" label="Synonymous type" optional="true" help="Keep only synonymous, non-synonymous SNP"> <option value="" selected="true">All</option> <option value="s">Synonymous</option> <option value="n">Non-synonymous</option> </param> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout" type="data" format="vcf" label="${fileout_label}.vcf" /> </outputs> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="filein" value="sample.vcf" /> <param name="genelist" value="accession.txt" /> <param name="feature" value="INTRON" /> <output name="fileout" file="result.vcf" /> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. class:: infomark **Authors** --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep. --------------------------------------------------- ====================== Filter And Convert VCF ====================== ----------- Description ----------- Filter VCF file and convert in Fasta, Hapmap and PED ----------------- Workflow position ----------------- **Upstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= **Downstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= ---------- Input file ---------- VCF file VCF file with all SNPs Genelist File listing the genes or individuals to be filtered. Gene_id or accesion number can be put in a file, one line per individual ---------- Parameters ---------- Output file name Prefix for the output VCF file Genomic feature Filter on genomic feature : Exon,INTRON,UTR_3_PRIME,UTR_5_PRIME,DOWNSTREAM,UPSTREAM or INTERGENIC Synonymous type Keep only synonymous, non-synonymous. ------------ Output files ------------ VCF file VCF file filtered --------------------------------------------------- --------------- Working example --------------- Input files =========== VCF file --------- :: #fileformat=VCFv4.1 #FILTER=<ID=LowQual,Description="Low quality"> #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> [...] CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 Genelist --------- :: Cc01g00020 Cc01g00010 Parameters ========== Output name -> filtered_genelist_intron Genomic feature -> Intron Output files ============ filtered_genelist_intron.vcf ---------------------------- :: #fileformat=VCFv4.1 #FILTER=<ID=LowQual,Description="Low quality"> #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> [...] CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0 </help> </tool>