Mercurial > repos > gandres > vcftools_filter_stats_diversity
diff vcftools_main/VCFToolsStats/.svn/text-base/vcfToolsStats.xml.svn-base @ 0:3b1436a9a6e5 draft
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author | gandres |
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date | Thu, 02 Jul 2015 05:21:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_main/VCFToolsStats/.svn/text-base/vcfToolsStats.xml.svn-base Thu Jul 02 05:21:40 2015 -0400 @@ -0,0 +1,214 @@ +<tool id="sniplay_vcftoolsstats" name="VCF tools Stats" 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> + <requirement type="package" version="0.1.12b">vcftools</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"> + vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> + <param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" /> + <data name="fileout_het" format="txt" label="${fileout_label}.het" /> + <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> + <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> + <data name="filelog" format="txt" label="${fileout_label}.log" /> + </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" /> + <output name="fileout_annot" file="result.annotation" /> + <output name="fileout_het" file="result.het" /> + <output name="fileout_imiss" file="result.imiss" /> + <output name="fileout_sum" file="result.TsTv.summary" /> + <output name="filelog" file="result.log" /> + </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. + +--------------------------------------------------- + +================ +VCF tools filter +================ + +----------- +Description +----------- + + Compute statistics on VCF file + +----------------- +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 + +---------- +Parameters +---------- + +Output file basename + Prefix for the output VCF file + +------------ +Output files +------------ + +.annotation file + Statistics on annotation/location along genome + +.het file + Statistics on heterozygosity of the individuals + +.imiss + Statistics on missing data of the inidividuals +.TsTv.summary + Statistics on mutation types and transition/transvertion number + +.log file + +--------------------------------------------------- + +--------------- +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 + + +Parameters +========== + +Output name -> vcf_stat + + +Output files +============ + +.annotation file +---------------- + +:: + + Genic 4489 + Intergenic 466 + ======== + Intron 960 + Exon 3248 + UTR 281 + ======== + Non-syn 226 + Synonym 3022 + +.het file +--------- + +:: + + INDV O(HOM) E(HOM) N_SITES F + CATB1 0 0.0 3616 0.00000 + +.imiss file +----------- + +:: + + INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS + CATB1 4813 0 0 0 + +.TsTv.summary file +------------------ + +:: + + MODEL COUNT + AC 371 + AG 1467 + AT 562 + CG 330 + CT 1659 + GT 397 + Ts 3126 + Tv 1660 + + + </help> + +</tool>