Mercurial > repos > matthias > dada2_plotqualityprofile
diff dada2_plotQualityProfile.xml @ 3:cf166b8a8e27 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
| author | matthias |
|---|---|
| date | Mon, 29 Apr 2019 08:57:18 -0400 |
| parents | 4095456821e2 |
| children | 863ebf0d28d5 |
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--- a/dada2_plotQualityProfile.xml Tue Apr 09 07:03:51 2019 -0400 +++ b/dada2_plotQualityProfile.xml Mon Apr 29 08:57:18 2019 -0400 @@ -11,25 +11,24 @@ <configfiles> <configfile name="dada2_script"><![CDATA[ files = c() -#if "batch" in $paired_cond.paired_select - #if "single" in $paired_cond.paired_select - files = c(files, '$reads') - #else - files = c(files, '$reads.forward') - files = c(files, '$reads.reverse') - #end if +#if "batch" in str($paired_cond.paired_select) + #if "single" in str($paired_cond.paired_select) + files = c(files, '$paired_cond.reads') + #else + files = c(files, '$paired_cond.reads.forward') + files = c(files, '$paired_cond.reads.reverse') + #end if #else - #for $read in $paired_cond.reads: - #if $paired_cond.paired_select == "no" - files = c(files, '$read') - #else - files = c(files, '$read.forward') - files = c(files, '$read.reverse') - #end if - #end for + #for $read in $paired_cond.reads: + #if "single" in str($paired_cond.paired_select) + files = c(files, '$read') + #else + files = c(files, '$read.forward') + files = c(files, '$read.reverse') + #end if + #end for #end if - library(ggplot2, quietly=T) library(dada2, quietly=T) @@ -37,64 +36,83 @@ #if str($n) != "" n=$n, #end if - aggregate = $mode) + aggregate = $aggregate) ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) ]]></configfile> </configfiles> <inputs> - <conditional name="paired_cond"> - <param name="paired_select" type="select" label="Input data organisation and processing mode" help="Select if data is organized in a paired collection or not (note that the pairing of the data sets is not used by the tool); batch will create a separate pdf for each input data set or data set pair; non-batch will create one pdf containing a plot for each data set"> - <option value="paired">paired - non batch</option> - <option value="single">single - non batch</option> - <option value="paired_batch">paired - batch</option> - <option value="single_batch">single - batch</option> - </param> - <when value="paired"> - <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> - </when> - <when value="single"> - <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> - </when> - <when value="paired_batch"> - <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> - </when> - <when value="single_batch"> - <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> - </when> - </conditional> - <param name="mode" 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 name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/> + <conditional name="paired_cond"> + <param name="paired_select" type="select" label="Input data organisation and processing mode" help="Select if data is organized in a paired collection or not (note that the pairing of the data sets is not used by the tool); batch will create a separate pdf for each input data set or data set pair; non-batch will create one pdf containing a plot for each data set"> + <option value="paired">paired - non batch</option> + <option value="single">single - non batch</option> + <option value="paired_batch">paired - batch</option> + <option value="single_batch">single - batch</option> + </param> + <when value="paired"> + <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> + </when> + <when value="single"> + <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> + </when> + <when value="paired_batch"> + <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> + </when> + <when value="single_batch"> + <param name="reads" type="data" format="fastqsanger,fastqsanger.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"/> </outputs> <tests> + <!-- paired non-batch, aggregate --> <test> - <param name="mode" value="TRUE"/> - <conditional name="paired_cond"> - <param name="paired_select" value="TRUE"/> - <param name="reads"> - <collection type="paired"> - <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> - <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> - </collection> - </param> - </conditional> + <param name="aggregate" value="TRUE"/> + <param name="paired_cond|paired_select" value="paired"/> + <param name="paired_cond|reads"> + <collection type="list:paired"> + <element name="F3D0_S188_L001"> + <collection type="paired"> + <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> + <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> + </collection> + </element> + </collection> + </param> <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/> </test> + <!-- paired, batch, no aggregate--> <test> - <param name="mode" value="FALSE"/> - <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> + <param name="aggregate" value="FALSE"/> + <param name="paired_cond|paired_select" value="paired_batch"/> + <param name="paired_cond|reads"> + <collection type="paired"> + <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> + <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> + </collection> + </param> <output name="output" value="qualityProfile.pdf" ftype="pdf"/> </test> + <!-- single, non-batch, aggregate --> <test> - <param name="mode" value="FALSE"/> - <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> + <param name="aggregate" value="TRUE"/> + <param name="paired_cond|paired_select" value="single"/> + <param name="paired_cond|reads" 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"/> </test> - </tests> + <!-- single, batch, no aggregate --> + <test> + <param name="aggregate" value="FALSE"/> + <param name="paired_cond|paired_select" value="single_batch"/> + <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> + <param name="n" value="10000"/> + <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ Summary .......