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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
author | iuc |
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date | Fri, 30 Jun 2023 07:58:07 +0000 |
parents | 2a90d2fd3336 |
children | fe1c3b7e4762 |
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<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09"> <description>plot a visual summary of the quality scores</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ ##name files by linking #import re mkdir forward && #if $batch_cond.paired_cond.paired_select != "single" mkdir reverse && #end if #if $batch_cond.batch_select == "batch": #set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier)) #if $batch_cond.paired_cond.paired_select != "paired" ln -s '$batch_cond.paired_cond.reads' forward/'$elid' && #else ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' && ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' && #end if #if $batch_cond.paired_cond.paired_select == "separate" ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' && #end if #else #for $read in $batch_cond.paired_cond.reads: #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) #if $batch_cond.paired_cond.paired_select != "paired" ln -s '$read' forward/'$elid' && #else ln -s '$read.forward' forward/'$elid' && ln -s '$read.reverse' reverse/'$elid' && #end if #end for #if $batch_cond.paired_cond.paired_select == "separate" #for $read in $batch_cond.paired_cond.sdaer: #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) ln -s '$read' reverse/'$elid' && #end for #end if #end if Rscript --slave '$dada2_script' ]]></command> <configfiles> <configfile name="dada2_script"><![CDATA[ #import re library(ggplot2, quietly=T) library(dada2, quietly=T) #if $batch_cond.batch_select != "batch" agg = $batch_cond.aggregate #else agg = FALSE #end if fwd_files = list.files("forward", full.names=T) qp <- plotQualityProfile(fwd_files, n=$n, aggregate = agg) ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) #if $batch_cond.paired_cond.paired_select != "single" rev_files = list.files("reverse", full.names=T) qp <- plotQualityProfile(rev_files, n=$n, aggregate = agg) ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm")) #end if ]]></configfile> </configfiles> <inputs> <conditional name="batch_cond"> <param name="batch_select" type="select" label="Processing mode" help="Joint processing processes all reads at once in a single job creating a single output (two in the case of paired data). Batch processes the samples in separate jobs and creates separate output for each"> <option value="joint">Joint</option> <option value="batch">Batch</option> </param> <when value="joint"> <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/> <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="batch"> <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/> </when> </conditional> <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"> <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter> </data> <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads"> <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter> </data> <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads"> <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter> </data> </outputs> <tests> <!-- all tests are against the same file using a delta that should ensure that the pdf contains a plot --> <!-- paired joint, no-aggregate --> <test expect_num_outputs="2"> <param name="batch_cond|batch_select" value="joint"/> <param name="batch_cond|paired_cond|paired_select" value="paired"/> <param name="batch_cond|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> <element name="F3D141_S207_L001"> <collection type="paired"> <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> </collection> </element> </collection> </param> <param name="batch_cond|aggregate" value="FALSE"/> <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/> <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf" compare="sim_size" delta="15000"/> </test> <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) --> <test expect_num_outputs="2"> <param name="batch_cond|batch_select" value="joint"/> <param name="batch_cond|paired_cond|paired_select" value="separate"/> <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> <param name="batch_cond|aggregate" value="FALSE"/> <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/> <output name="output_rev" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/> </test> <!-- single, non-batch, aggregate, small sample --> <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="joint"/> <param name="batch_cond|paired_cond|paired_select" value="single"/> <param name="batch_cond|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"/> <param name="batch_cond|aggregate" value="TRUE"/> <output name="output" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="16000"/> </test> <!-- paired, batch --> <test expect_num_outputs="2"> <param name="batch_cond|batch_select" value="batch"/> <param name="batch_cond|paired_cond|paired_select" value="paired"/> <param name="batch_cond|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_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/> <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/> </test> <!-- paired-separate batch (sim_size because element ids differ)--> <test expect_num_outputs="2"> <param name="batch_cond|batch_select" value="batch"/> <param name="batch_cond|paired_cond|paired_select" value="separate"/> <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/> <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/> </test> <!-- single, batch --> <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="batch"/> <param name="batch_cond|paired_cond|paired_select" value="single"/> <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> <param name="n" value="10000"/> <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/> </test> </tests> <help><![CDATA[ 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. @HELP_OVERVIEW@ ]]></help> <expand macro="citations"/> </tool>