Mercurial > repos > matthias > dada2_learnerrors

comparison dada2_learnErrors.xml @ 7:382900945187 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
author matthias
date Mon, 27 May 2019 05:32:43 -0400
parents 9aeea74a1fc9
children ef3ebaa70032
comparison
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6:f9040a48d23f 7:382900945187
32 plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.err_out, err_in = $plotopt.err_in, nominalQ = $plotopt.nominalQ) 32 plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.err_out, err_in = $plotopt.err_in, nominalQ = $plotopt.nominalQ)
33 ggsave('plot.pdf', plot, width = 20,height = 15,units = c("cm")) 33 ggsave('plot.pdf', plot, width = 20,height = 15,units = c("cm"))
34 ]]></configfile> 34 ]]></configfile>
35 </configfiles> 35 </configfiles>
36 <inputs> 36 <inputs>
37 <param argument="fls" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data" help="forward or reverse reads should be processed separately"/> 37 <param argument="fls" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data" help="forward or reverse reads should be processed separately"/>
38 <param argument="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning"/> 38 <param argument="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning"/>
39 <section name="advanced" title="Advanced Option"> 39 <section name="advanced" title="Advanced Option">
40 <expand macro="errorEstimationFunction"/> 40 <expand macro="errorEstimationFunction"/>
41 <param argument="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Randomize samples" help="Pick samples at random, otherwise samples are read in the provided order until enough reads are obtained (default)."/> 41 <param argument="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Randomize samples" help="Pick samples at random, otherwise samples are read in the provided order until enough reads are obtained (default)."/>
42 <param name="maxconsist" argument="MAX_CONSIST" type="integer" value="10" min="0" label="Maximum number of times to step through the selfconsistency loop" help="If convergence was not reached in MAX_CONSIST steps, the estimated error rates in the last step are returned."/> 42 <param name="maxconsist" argument="MAX_CONSIST" type="integer" value="10" min="0" label="Maximum number of times to step through the selfconsistency loop" help="If convergence was not reached in MAX_CONSIST steps, the estimated error rates in the last step are returned."/>