Mercurial > repos > matthias > dada2_plotqualityprofile
changeset 8:7970dfbedde3 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 977f22125c9ad5c3c5560de8946017305c5633c1
author | matthias |
---|---|
date | Mon, 27 May 2019 13:23:01 -0400 |
parents | ec0479593908 |
children | d908015e5889 |
files | dada2_plotQualityProfile.xml macros.xml test-data/qualityProfileMultiple_rev.pdf test-data/qualityProfile_rev.pdf |
diffstat | 2 files changed, 43 insertions(+), 18 deletions(-) [+] |
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--- a/dada2_plotQualityProfile.xml Mon May 27 05:33:57 2019 -0400 +++ b/dada2_plotQualityProfile.xml Mon May 27 13:23:01 2019 -0400 @@ -33,37 +33,52 @@ <configfiles> <configfile name="dada2_script"><![CDATA[ #import re -files = c() +fwd_files = c() +rev_files = c() #if "batch" in str($paired_cond.paired_select) #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier)) #if "single" in str($paired_cond.paired_select) - files = c(files, '$elid') + fwd_files = c(fwd_files, '$elid') #else - files = c(files, paste('$elid', 'forward', sep = "_")) - files = c(files, paste('$elid', 'reverse', sep = "_")) + fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_")) + rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_")) #end if #else #for $read in $paired_cond.fl: #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) #if "single" in str($paired_cond.paired_select) - files = c(files, '$elid') + fwd_files = c(fwd_files, '$elid') #else - files = c(files, paste('$elid', 'forward', sep = "_")) - files = c(files, paste('$elid', 'reverse', sep = "_")) + fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_")) + rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_")) #end if #end for #end if +#if not "batch" in str($paired_cond.paired_select) +agg = $paired_cond.aggregate +#else +agg = FALSE +#end if + library(ggplot2, quietly=T) library(dada2, quietly=T) -qp <- plotQualityProfile(files, +qp <- plotQualityProfile(fwd_files, #if str($n) != "" n=$n, #end if - aggregate = $aggregate) + aggregate = agg) +ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) -ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) +#if "paired" in str($paired_cond.paired_select) +qp <- plotQualityProfile(rev_files, +#if str($n) != "" + n=$n, +#end if + aggregate = agg) +ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm")) +#end if ]]></configfile> </configfiles> <inputs> @@ -76,9 +91,11 @@ </param> <when value="paired"> <param argument="fl" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="Short read data"/> + <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/> </when> <when value="single"> <param argument="fl" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data"/> + <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/> </when> <when value="paired_batch"> <param argument="fl" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Short read data"/> @@ -87,17 +104,24 @@ <param argument="fl" type="data" format="fastq,fastq.gz" label="Short read data"/> </when> </conditional> - <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/> <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> </inputs> <outputs> - <data name="output" format="pdf" from_work_dir="output.pdf"/> + <data name="output" format="pdf" from_work_dir="output.pdf"> + <filter>"single" in paired_cond['paired_select']</filter> + </data> + <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads"> + <filter>"paired" in paired_cond['paired_select']</filter> + </data> + <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads"> + <filter>"paired" in paired_cond['paired_select']</filter> + </data> </outputs> <tests> <!-- paired non-batch, aggregate --> <test> - <param name="aggregate" value="TRUE"/> <param name="paired_cond|paired_select" value="paired"/> + <param name="paired_cond|aggregate" value="TRUE"/> <param name="paired_cond|fl"> <collection type="list:paired"> <element name="F3D0_S188_L001"> @@ -108,11 +132,11 @@ </element> </collection> </param> - <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/> + <output name="output_fwd" value="qualityProfileMultiple.pdf" ftype="pdf"/> + <output name="output_rev" value="qualityProfileMultiple_rev.pdf" ftype="pdf"/> </test> <!-- paired, batch, no aggregate--> <test> - <param name="aggregate" value="FALSE"/> <param name="paired_cond|paired_select" value="paired_batch"/> <param name="paired_cond|fl"> <collection type="paired"> @@ -120,12 +144,13 @@ <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> </collection> </param> - <output name="output" value="qualityProfile.pdf" ftype="pdf"/> + <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf"/> + <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf"/> </test> <!-- single, non-batch, aggregate --> <test> - <param name="aggregate" value="TRUE"/> <param name="paired_cond|paired_select" value="single"/> + <param name="paired_cond|aggregate" value="TRUE"/> <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> <param name="n" value="10000"/> <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
--- a/macros.xml Mon May 27 05:33:57 2019 -0400 +++ b/macros.xml Mon May 27 13:23:01 2019 -0400 @@ -69,7 +69,7 @@ <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/> <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/> <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/> - <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/> + <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/> </section> </xml> <xml name="filters">