Mercurial > repos > dereeper > sniplay
diff hapmap2mlmm/HapmapToMLMMFiles.xml @ 3:345f88a8f483 draft
Uploaded
author | dereeper |
---|---|
date | Fri, 10 Jul 2015 10:38:43 -0400 |
parents | 420b57c3c185 |
children | 10627af23f10 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmap2mlmm/HapmapToMLMMFiles.xml Fri Jul 10 10:38:43 2015 -0400 @@ -0,0 +1,158 @@ +<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> + <description>converts a hapmap file into MLMM input files</description> + <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot + </command> + <inputs> + <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> + </inputs> + <outputs> + <data format="txt" name="snp_info" label="SNP Info file"/> + <data format="txt" name="genot" label="Genotyping file for MLMM"/> + </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 --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + + + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** South Green. + +--------------------------------------------------- + + +================= +HapmapToMLMMFiles +================= + +----------- +Description +----------- + + | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Fasta alignment fasta +=============== ====================== =========== + + +**Downstream tool** + +=========== ========================== ======= +Name input file(s) format +=========== ========================== ======= +MLMM +=========== ========================== ======= + + + +---------- +Input file +---------- + +Hapmap file + Allelic file in Hapmap format + + + +------------ +Output files +------------ + +SNP Info file + +Genotyping file for MLMM + + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA + + +Output files +============ + +SNP Info file +------------- + +:: + + SNP Chr Pos + SNP1 1 3102 + SNP2 1 4648 + SNP3 1 7601 + + +Genotyping file for MLMM +------------------------ + +:: + + Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14 + Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0 + Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>