Mercurial > repos > matthias > dada2_plotqualityprofile
view dada2_plotQualityProfile.xml @ 0:de5c51e1c190 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author | matthias |
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date | Fri, 08 Mar 2019 06:35:24 -0500 |
parents | |
children | 4095456821e2 |
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<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@"> <description>plot a visual summary of the quality scores</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ Rscript --slave '$dada2_script' ]]></command> <configfiles> <configfile name="dada2_script"><![CDATA[ files = c() #if $mode_cond.mode_select == "TRUE" #for $read in $mode_cond.reads: files = c(files, '$read') #end for #else files = c(files, '$mode_cond.reads') #end if library(ggplot2, quietly=T) library(dada2, quietly=T) qp <- plotQualityProfile(files, #if str($n) != "" n=$n, #end if aggregate = $mode_cond.mode_select) ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) ]]></configfile> </configfiles> <inputs> <conditional name="mode_cond"> <param name="mode_select" type="select" label="Aggregate data" help="Create a single plot for all data sets (default) or a separate plot for each data set"> <option value="TRUE">yes</option> <option value="FALSE">no</option> </param> <when value="TRUE"> <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> </when> <when value="FALSE"> <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> </when> </conditional> <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/> </inputs> <outputs> <data name="output" format="pdf" from_work_dir="output.pdf"/> </outputs> <help><![CDATA[ TODO: Fill in help. ]]></help> <expand macro="citations"/> </tool>