comparison stacks_genotypes.xml @ 10:00f4a4e553ae draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 689ccfe1532a4de7b60fe69cd3945601d76aefb6"

9:5af94af9ec8f

        <section name="advanced_options" title="advanced options" expanded="False">
            <param name="minprogeny" type="integer" value="0" optional="true" argument="-r" label="Minimum number of progeny required to print a marker" />
            <param name="mindepth" type="integer" value="" optional="true" argument="-m" label="Minimum stack depth required before exporting a locus in a particular individual" />
            <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />

            <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted markers to include in the export" />
            <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" />

            <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." />

            <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" />
        </section>

10:00f4a4e553ae

        <section name="advanced_options" title="advanced options" expanded="False">
            <param name="minprogeny" type="integer" value="0" optional="true" argument="-r" label="Minimum number of progeny required to print a marker" />
            <param name="mindepth" type="integer" value="" optional="true" argument="-m" label="Minimum stack depth required before exporting a locus in a particular individual" />
            <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />

            <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" />
            <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" />

            <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." />

            <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" />
        </section>