Mercurial > repos > dereeper > plink
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author | dereeper |
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date | Wed, 07 Feb 2018 00:15:42 -0500 |
parents | 6d1122b57344 |
children | d6a7be1b5adb |
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<tool id="sniplay_plink" name="plink" version="1.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> - Filter large VCF file</description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.90b4">plink</requirement> </requirements> <!-- [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> <!-- [REQUIRED] The command to execute --> <command interpreter="bash"> ./plink.sh $vcf $fileout $filelog $frequency $max_freq $allow_missing $type_p $bound_start $bound_end #if str( $samples ) == "": 'None' #else $samples #end if #if str( $chromosomes ) == "": 'None' #else $chromosomes #end if </command> <code file="find_indiv.py"/> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" /> <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." /> <!--<param name="samples" type="text" label="Samples" multiple="true" help="Samples to be analyzed." />--> <!--<param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />--> <param name="frequency" type="float" value="0" label="Minimum MAF" help="Minimum Minor Allele Frequency (MAF)" /> <param name="max_freq" type="float" value="0.5" label="Maximum MAF" help="Maximum Minor Allele Frequency (MAF)" /> <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." /> <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." > <option value="ALL" selected="true">All</option> <option value="SNP">SNPs only</option> </param> <param name="chromosomes" type="text" label="Chromosomes" multiple="true" help="Chromosomes to be analyzed. (Comma-separated list of reference sequences, ex: Chr1,Chr2)" /> <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." /> <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout" format="vcf" label="Plink filtered VCF"/> <data name="filelog" format="txt" label="Plink logfile" /> </outputs> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. class:: infomark **Authors** Shaun Purcell : plink_ .. _plink: https://www.cog-genomics.org/plink2 | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, **American Journal of Human Genetics**, 2007 .. class:: infomark **Galaxy integration** Dereeper Alexis (IRD), 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 </help> </tool>