Mercurial > repos > matthias > dada2_plotqualityprofile
diff dada2_plotQualityProfile.xml @ 2:4095456821e2 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
| author | matthias |
|---|---|
| date | Tue, 09 Apr 2019 07:03:51 -0400 |
| parents | de5c51e1c190 |
| children | cf166b8a8e27 |
line wrap: on
line diff
--- a/dada2_plotQualityProfile.xml Fri Mar 08 08:34:49 2019 -0500 +++ b/dada2_plotQualityProfile.xml Tue Apr 09 07:03:51 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@"> +<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@"> <description>plot a visual summary of the quality scores</description> <macros> <import>macros.xml</import> @@ -11,47 +11,103 @@ <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 +#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 #else - files = c(files, '$mode_cond.reads') + #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 #end if + library(ggplot2, quietly=T) library(dada2, quietly=T) qp <- plotQualityProfile(files, #if str($n) != "" - n=$n, + n=$n, #end if - aggregate = $mode_cond.mode_select) + aggregate = $mode) 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> + <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)"/> </inputs> <outputs> <data name="output" format="pdf" from_work_dir="output.pdf"/> </outputs> - + <tests> + <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> + <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/> + </test> + <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"/> + <output name="output" value="qualityProfile.pdf" ftype="pdf"/> + </test> + <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="n" value="10000"/> + <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> + </test> + </tests> <help><![CDATA[ - TODO: Fill in help. +Summary +....... + +This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq datasets. + +Details +....... + +The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles. If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend +to at least that position. + +Note this tool ignores the pairing of the reads, but the data is just processed as list. ]]></help> <expand macro="citations"/> </tool>