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date | Mon, 24 Aug 2015 09:29:12 +0000 |
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<tool id="STACKSassembleperead" name="STACKS : assemble read pairs by locus" version="1.1.1"> <description>Run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description> <requirements> <requirement type="package" version="1.18">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> </requirements> <command interpreter="python"> STACKS_sort_read_pairs.py -a $STACKS_archive -e $samples_archive #if str( $options_whitelist.whitelist_selector) == "yes" -b $whitelist #end if #if str( $options_filter.reads_selector) == "yes" -c $options_filter.threshold #end if #if str( $options_filter2.length_selector) == "yes" -d $options_filter2.threshold2 #end if -o $output </command> <inputs> <param name="STACKS_archive" format="zip,tar.gz" type="data" label="Archive from STACKS pipeline regrouping all outputs" /> <param name="samples_archive" format="zip,fastq.gz,tar.gz,tar.bz2" type="data" label="Archive with raw reads used to execute previous STACKS pipeline" /> <conditional name="options_whitelist"> <param name="whitelist_selector" type="select" label="Have you got a whitelist?" > <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"></when> <when value="yes"> <param name="whitelist" format="txt, tabular" type="data" label="Whitelist file containing loci that we want to assemble: those that have SNPs" /> </when> </conditional> <conditional name="options_filter"> <param name="reads_selector" type="select" label="Specify a treshold for the minimum number of reads by locus?" > <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"></when> <when value="yes"> <param name="threshold" type="integer" value="10" label="Minimum number of reads by locus"/> </when> </conditional> <conditional name="options_filter2"> <param name="length_selector" type="select" label="Specify a minimum length for asssembled contigs?" > <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"></when> <when value="yes"> <param name="threshold2" type="integer" value="200" label="Minimum length for asssembled contigs"/> </when> </conditional> </inputs> <outputs> <data format="fasta" name="output" label="collated.fa : ${tool.name} on ${on_string}" /> </outputs> <stdio> <exit_code range="1" level="fatal" description="Error" /> </stdio> <help> .. class:: infomark **What it does** This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results -------- **Created by:** Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko -------- **Example:** Input file: Output archives of STACKS : Reference map or STACKS : De novo map, in zip or tar.gz format Output file: A collated.fa file containing assembled contigs for each locus Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki <https://www.e-biogenouest.org/wiki/ManArchiveGalaxy>`_ . -------- **Project links:** `STACKS website <http://creskolab.uoregon.edu/stacks/>`_ . `STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ . `STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ . -------- **References:** -J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013. -J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013. -J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011. -A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011. -P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011. -K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010. -------- **Integrated by:** Yvan Le Bras and Cyril Monjeaud GenOuest Bio-informatics Core Facility UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) support@genouest.org If you use this tool in Galaxy, please cite : `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ </help> <citations> <citation type="doi">10.1111/mec.12354</citation> <citation type="doi">10.1111/mec.12330</citation> <citation type="doi">10.1534/g3.111.000240</citation> <citation type="doi">10.1534/genetics.111.127324</citation> <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> <citation type="doi">10.1073/pnas.1006538107</citation> <citation type="bibtex">@INPROCEEDINGS{JOBIM2013, author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, booktitle = {JOBIM 2013 Proceedings}, year = {2013}, url = {https://www.e-biogenouest.org/resources/128}, pages = {97-106} }</citation> </citations> </tool>