Mercurial > repos > matthias > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 0:de5c51e1c190 draft

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author matthias
date Fri, 08 Mar 2019 06:35:24 -0500
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children 4095456821e2
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de5c51e1c190 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@">
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2 <description>plot a visual summary of the quality scores</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 Rscript --slave '$dada2_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="dada2_script"><![CDATA[
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13 files = c()
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14 #if $mode_cond.mode_select == "TRUE"
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15 #for $read in $mode_cond.reads:
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16 files = c(files, '$read')
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17 #end for
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18 #else
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19 files = c(files, '$mode_cond.reads')
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20 #end if
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21
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22 library(ggplot2, quietly=T)
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23 library(dada2, quietly=T)
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24
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25 qp <- plotQualityProfile(files,
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26 #if str($n) != ""
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27 n=$n,
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28 #end if
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29 aggregate = $mode_cond.mode_select)
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30
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31 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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32 ]]></configfile>
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33 </configfiles>
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34 <inputs>
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35 <conditional name="mode_cond">
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36 <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">
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37 <option value="TRUE">yes</option>
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38 <option value="FALSE">no</option>
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39 </param>
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40 <when value="TRUE">
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41 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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42 </when>
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43 <when value="FALSE">
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44 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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45 </when>
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46 </conditional>
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47 <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/>
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48 </inputs>
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49 <outputs>
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50 <data name="output" format="pdf" from_work_dir="output.pdf"/>
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51 </outputs>
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52
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53 <help><![CDATA[
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54 TODO: Fill in help.
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55 ]]></help>
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56 <expand macro="citations"/>
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57 </tool>