Mercurial > repos > matthias > dada2_learnerrors

annotate dada2_learnErrors.xml @ 0:56d5be6c03b9 draft

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author matthias
date Fri, 08 Mar 2019 06:30:11 -0500
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children 57eb7437f646
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1 <tool id="dada2_learnErrors" name="dada2: learnErrors" version="@DADA2_VERSION@">
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2 <description>Learn Error rates</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #for $read in $reads:
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10 ln -s '$read' '$read.element_identifier' &&
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11 #end for
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12 mkdir '$errors.extra_files_path' &&
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13 Rscript '$dada2_script' \${GALAXY_SLOTS:-1}
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="dada2_script"><![CDATA[
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17 library(ggplot2, quietly=T)
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18 library(dada2, quietly=T)
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20 args <- commandArgs(trailingOnly = TRUE)
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21 nthreads <- as.integer(args[1])
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23 files <- c()
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24 #for $read in $reads:
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25 files <- c(files, '$read.element_identifier')
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26 #end for
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28 err <- learnErrors(files, nbases = 10**$nbases,
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29 errorEstimationFunction = $advanced.errfoo, multithread = nthreads,
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30 randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)
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32 write.table(err\$err_out, file = '$errors', quote = F, sep = "\t", row.names = T, col.names = F)
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33 saveRDS(err, file=file.path('$errors.extra_files_path', "Rdata"))
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34
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35
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36 ## generate error plots
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37 plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.errout, err_in = $plotopt.errin, nominalQ = $plotopt.nominalQ)
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38 ggsave('output.pdf', plot, width = 20,height = 15,units = c("cm"))
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39 ]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data" help="forward or reverse reads should be processed separately"/>
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43 <param name="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning" help=""/>
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44 <section name="advanced" title="Advanced Option">
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45 <expand macro="errorEstimationFunction"/>
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46 <param name="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="randomize samples"/>
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47 <param name="maxconsist" type="integer" value="10" min="0" label="maximum number of times to step through the selfconsistency loop" help=""/>
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48 <param name="omegac" type="integer" value="0" min="0" label="threshold at which unique sequences inferred to contain errors are corrected" help=""/>
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49 </section>
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50 <section name="plotopt" title="Plotting Option">
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51 <param name="obs" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot observed error rates"/>
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52 <param name="errout" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot output error rates"/>
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53 <param name="errin" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="plot input error rates"/>
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54 <param name="nominalQ" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot observed error rates"/>
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55 </section>
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56
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57 </inputs>
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58 <outputs>
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59 <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/>
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60 <data name="output" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: error rates plot"/>
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61 </outputs>
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62
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63 <help><![CDATA[
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64 TODO: Fill in help.
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65 ]]></help>
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66 <expand macro="citations"/>
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67 </tool>