Mercurial > repos > dereeper > sniplay
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author | dereeper |
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date | Fri, 10 Jul 2015 10:38:11 -0400 |
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<tool id="sniplay_rooting" name="Rooting" version="1.0.2"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Midpoint rooting of newick tree </description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package">Rootings_54.jar</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"> Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> <data name="fileout" type="data" format="txt" label="${fileout_label}" /> </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="newick" /> <output name="fileout" file="out_tree" /> <output name="fileout_log" file="out_tree.log" /> </test> <!-- [HELP] Multiple tests can be defined with different parameters --> <!-- <test> </test> --> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. class:: infomark **Authors** Jean-François Dufayard, CIRAD, South Green platform .. 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 .. class:: infomark **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). --------------------------------------------------- ======= Rooting ======= ----------- Description ----------- Compute a midpoint newick rooted tree. ----------------- Workflow position ----------------- **Upstream tool** =========== ========================== ======= Name output file(s) format =========== ========================== ======= fastme Newick tree Newick =========== ========================== ======= ---------- Input file ---------- Newick file ---------- Parameters ---------- Output name Output base name for the ouput files ------------ Output files ------------ Output_name Resulting tree rooted in newick format Output_name.log Log file ------------ Dependencies ------------ Rooting CIRAD tool. Contact jean-francois.dufayard@cirad.fr --------------------------------------------------- --------------- Working example --------------- Input files =========== Newick file ----------- :: (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... Parameters ========== Output name -> out tree Output files ============ out tree -------- :: (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... </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>