Mercurial > repos > iuc > dada2_learnerrors

comparison dada2_learnErrors.xml @ 2:c48d42d65d2b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
author iuc
date Mon, 16 Mar 2020 07:44:03 -0400
parents 39638e0aff59
children afdfa35a89d9
comparison
equal deleted inserted replaced
1:39638e0aff59 2:c48d42d65d2b
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="fastq,fastq.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="Magnitude 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."/>
43 <param name="omegac" argument="OMEGA_C" type="float" value="0" min="0" label="Threshold at which unique sequences inferred to contain errors are corrected" help="For reasons of convergence, and because it is 43 <param name="omegac" argument="OMEGA_C" type="float" value="0" min="0" label="Threshold at which unique sequences inferred to contain errors are corrected" help="For reasons of convergence, and because it is
55 <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/> 55 <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/>
56 <data name="plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}: error rates plot"/> 56 <data name="plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}: error rates plot"/>
57 </outputs> 57 </outputs>
58 <tests> 58 <tests>
59 <test> 59 <test>
60 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz"/> 60 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz,filterAndTrim_F3D141_R1.fq.gz" ftype="fastqsanger.gz"/>
61 <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="7000"/> 61 <output name="errors" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="7000"/>
62 <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" compare="sim_size" delta="5000" /> 62 <output name="plot" value="learnErrors_R1.pdf" ftype="pdf" compare="sim_size" delta="5000" />
63 </test> 63 </test>
64 <!-- test w non-default parameters --> 64 <!-- test w non-default parameters -->
65 <test> 65 <test>
66 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz"/> 66 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz,filterAndTrim_F3D141_R1.fq.gz" ftype="fastqsanger.gz"/>
67 <param name="nbases" value="6" /> 67 <param name="nbases" value="6" />
68 <param name="advanced|errfoo" value="noqualErrfun" /> 68 <param name="advanced|errfoo" value="noqualErrfun" />
69 <param name="advanced|randomize" value="TRUE" /> 69 <param name="advanced|randomize" value="TRUE" />
70 <param name="advanced|maxconsist" value="5" /> 70 <param name="advanced|maxconsist" value="5" />
71 <param name="advanced|omegac" value="1e-10" /> 71 <param name="advanced|omegac" value="1e-10" />
72 <param name="plotopt|obs" value="FALSE" /> 72 <param name="plotopt|obs" value="FALSE" />
73 <param name="plotopt|err_out" value="FALSE" /> 73 <param name="plotopt|err_out" value="FALSE" />
74 <param name="plotopt|err_in" value="TRUE" /> 74 <param name="plotopt|err_in" value="TRUE" />
75 <param name="plotopt|nominalQ" value="FALSE"/> 75 <param name="plotopt|nominalQ" value="FALSE"/>
76 <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="13000"/> 76 <output name="errors" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="13000"/>
77 <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" compare="sim_size" delta="5000" /> 77 <output name="plot" value="learnErrors_R1.pdf" ftype="pdf" compare="sim_size" delta="5000" />
78 </test> 78 </test>
79 <!-- TODO test w multiple inputs -->
80 </tests> 79 </tests>
81 <help><![CDATA[ 80 <help><![CDATA[
82 Description 81 Description
83 ........... 82 ...........
84 83