<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" default_identifier_source="batch_cond|paired_cond|reads" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
            <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
        </data>
        <data name="output_rev" format="pdf" default_identifier_source="batch_cond|paired_cond|sdaer" from_work_dir="output_rev.pdf" label="${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>