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comparison dada2_learnErrors.xml @ 0:56d5be6c03b9 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author matthias
date Fri, 08 Mar 2019 06:30:11 -0500
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children 57eb7437f646
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-1:000000000000 0:56d5be6c03b9
1 <tool id="dada2_learnErrors" name="dada2: learnErrors" version="@DADA2_VERSION@">
2 <description>Learn Error rates</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #for $read in $reads:
10 ln -s '$read' '$read.element_identifier' &&
11 #end for
12 mkdir '$errors.extra_files_path' &&
13 Rscript '$dada2_script' \${GALAXY_SLOTS:-1}
14 ]]></command>
15 <configfiles>
16 <configfile name="dada2_script"><![CDATA[
17 library(ggplot2, quietly=T)
18 library(dada2, quietly=T)
19
20 args <- commandArgs(trailingOnly = TRUE)
21 nthreads <- as.integer(args[1])
22
23 files <- c()
24 #for $read in $reads:
25 files <- c(files, '$read.element_identifier')
26 #end for
27
28 err <- learnErrors(files, nbases = 10**$nbases,
29 errorEstimationFunction = $advanced.errfoo, multithread = nthreads,
30 randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)
31
32 write.table(err\$err_out, file = '$errors', quote = F, sep = "\t", row.names = T, col.names = F)
33 saveRDS(err, file=file.path('$errors.extra_files_path', "Rdata"))
34
35
36 ## generate error plots
37 plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.errout, err_in = $plotopt.errin, nominalQ = $plotopt.nominalQ)
38 ggsave('output.pdf', plot, width = 20,height = 15,units = c("cm"))
39 ]]></configfile>
40 </configfiles>
41 <inputs>
42 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data" help="forward or reverse reads should be processed separately"/>
43 <param name="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning" help=""/>
44 <section name="advanced" title="Advanced Option">
45 <expand macro="errorEstimationFunction"/>
46 <param name="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="randomize samples"/>
47 <param name="maxconsist" type="integer" value="10" min="0" label="maximum number of times to step through the selfconsistency loop" help=""/>
48 <param name="omegac" type="integer" value="0" min="0" label="threshold at which unique sequences inferred to contain errors are corrected" help=""/>
49 </section>
50 <section name="plotopt" title="Plotting Option">
51 <param name="obs" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot observed error rates"/>
52 <param name="errout" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot output error rates"/>
53 <param name="errin" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="plot input error rates"/>
54 <param name="nominalQ" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="plot observed error rates"/>
55 </section>
56
57 </inputs>
58 <outputs>
59 <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/>
60 <data name="output" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: error rates plot"/>
61 </outputs>
62
63 <help><![CDATA[
64 TODO: Fill in help.
65 ]]></help>
66 <expand macro="citations"/>
67 </tool>