Mercurial > repos > matthias > dada2_plotqualityprofile
comparison 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 |
|---|---|
| date | Fri, 08 Mar 2019 06:35:24 -0500 |
| parents | |
| children | 4095456821e2 |
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| -1:000000000000 | 0:de5c51e1c190 |
|---|---|
| 1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@"> | |
| 2 <description>plot a visual summary of the quality scores</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 Rscript --slave '$dada2_script' | |
| 10 ]]></command> | |
| 11 <configfiles> | |
| 12 <configfile name="dada2_script"><![CDATA[ | |
| 13 files = c() | |
| 14 #if $mode_cond.mode_select == "TRUE" | |
| 15 #for $read in $mode_cond.reads: | |
| 16 files = c(files, '$read') | |
| 17 #end for | |
| 18 #else | |
| 19 files = c(files, '$mode_cond.reads') | |
| 20 #end if | |
| 21 | |
| 22 library(ggplot2, quietly=T) | |
| 23 library(dada2, quietly=T) | |
| 24 | |
| 25 qp <- plotQualityProfile(files, | |
| 26 #if str($n) != "" | |
| 27 n=$n, | |
| 28 #end if | |
| 29 aggregate = $mode_cond.mode_select) | |
| 30 | |
| 31 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) | |
| 32 ]]></configfile> | |
| 33 </configfiles> | |
| 34 <inputs> | |
| 35 <conditional name="mode_cond"> | |
| 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"> | |
| 37 <option value="TRUE">yes</option> | |
| 38 <option value="FALSE">no</option> | |
| 39 </param> | |
| 40 <when value="TRUE"> | |
| 41 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | |
| 42 </when> | |
| 43 <when value="FALSE"> | |
| 44 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data name="output" format="pdf" from_work_dir="output.pdf"/> | |
| 51 </outputs> | |
| 52 | |
| 53 <help><![CDATA[ | |
| 54 TODO: Fill in help. | |
| 55 ]]></help> | |
| 56 <expand macro="citations"/> | |
| 57 </tool> |