Mercurial > repos > dereeper > sniplay
diff SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml @ 3:345f88a8f483 draft
Uploaded
author | dereeper |
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date | Fri, 10 Jul 2015 10:38:43 -0400 |
parents | 420b57c3c185 |
children | 10627af23f10 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Fri Jul 10 10:38:43 2015 -0400 @@ -0,0 +1,207 @@ +<tool id="sniplay_density" name="SNP density" version="1.2.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Calculate SNP densities along chromosome from HapMap</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="bash"> + calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> + <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> + <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> + <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> + </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="input" value="input_test.txt" /> + <output name="output" file="output_test.txt" /> + </test> +--> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <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** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + + + +============= +SNP densities +============= + +----------- +Description +----------- + + Calculate SNP densities along chromosome from HapMap + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Hapmap file hapmap +=============== ====================== =========== + + +---------- +Input file +---------- + +Hapmap file + File with SNPs + + +---------- +Parameters +---------- + +Step + Step in bp for the window to calculate SNP density + +Output name + Output base name for the two ouput files + + +------------ +Output files +------------ + +Output_name + Tabular file with SNP density in each postion + +Output_name.by_sample + Tabular file with SNP density for each sample + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 + chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT + chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA + chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC + chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG + chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG + chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT + +Parameters +========== + +Step -> 200000 + +Output name -> densities + + +Output files +============ + +densities +--------- + +:: + + Chromosome Position SNPs + chr1 200000 355 + chr1 400000 228 + chr1 600000 63 + chr1 800000 191 + + +densities.by_sample +------------------- + +:: + + Chromosome BA58 BA59 BD54 + chr1 220 197 225 + chr1 130 119 133 + chr1 43 43 40 + chr1 139 167 141 + + </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>