Mercurial > repos > iuc > stacks_genotypes

comparison stacks_genotypes.xml @ 7:f8d5294dc678 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 42d47def94824c7a311b147c4fa8607c8d043a2f
author iuc
date Wed, 10 Oct 2018 10:12:32 -0400
parents bca0b38b0ac8
children d9a98a979632
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6:a4ba2695ac07 7:f8d5294dc678
115 <section name="advanced_options" title="advanced options" expanded="False"> 115 <section name="advanced_options" title="advanced options" expanded="False">
116 <param name="minprogeny" type="integer" value="0" optional="true" argument="-r" label="Minimum number of progeny required to print a marker" /> 116 <param name="minprogeny" type="integer" value="0" optional="true" argument="-r" label="Minimum number of progeny required to print a marker" />
117 <param name="mindepth" type="integer" value="" optional="true" argument="-m" label="Minimum stack depth required before exporting a locus in a particular individual" /> 117 <param name="mindepth" type="integer" value="" optional="true" argument="-m" label="Minimum stack depth required before exporting a locus in a particular individual" />
118 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" /> 118 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
119 119
120 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted markers to include in the export" /> 120 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" />
121 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing Blacklisted markers to be excluded from the export" /> 121 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" />
122 122
123 <param name="manual_cor" argument="--cor_path" type="data" format="tabular,txt" optional="true" label="Path to file containing manual genotype corrections from a Stacks SQL database to incorporate into output." /> 123 <param name="manual_cor" argument="--cor_path" type="data" format="tabular,txt" optional="true" label="Path to file containing manual genotype corrections from a Stacks SQL database to incorporate into output." />
124 124
125 <param name="batchid" type="integer" value="1" label="Batch ID to examine when exporting from the catalog" help="Only useful if you analyse data that was processed outside galaxy" /> 125 <param name="batchid" type="integer" value="1" label="Batch ID to examine when exporting from the catalog" help="Only useful if you analyse data that was processed outside galaxy" />
126 </section> 126 </section>