Mercurial > repos > dereeper > sniplay3
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filterVCFonAnnotations.xml Thu Feb 12 15:54:24 2015 -0500 @@ -0,0 +1,207 @@ +<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>