<tool id="multiqc" name="MultiQC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>aggregate results from bioinformatics analyses into a single report</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro='requirements' />
    <version_command>multiqc --version</version_command>
    <command detect_errors="aggressive">
<![CDATA[
#import re
#import os

die() { echo "$@" 1>&2 ; exit 1; } &&

mkdir multiqc_WDir &&

#set $configfile="F"

#for $i, $repeat in enumerate( $results )
    #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i))
    mkdir $software_dir &&
    #if str($repeat.software_cond.software) == "bamtools"
        #set $pattern = "Stats for BAM file(s)"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "bcftools"
        #set $pattern = "This file was produced by bcftools stats"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "bismark"
        @BISMARK_INPUT@
    #elif str($repeat.software_cond.software) == "bowtie2"
        #set $pattern = "% overall alignment rate"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "busco"
        ## Searches for files "short_summary_[samplename].txt"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "cutadapt"
        #set $pattern = "This is cutadapt"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
            ln -s '$file' '$file_path' &&
            ## replace header for old cutadapt release
            sed -i.old 's/You are running/This is/' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" &&
        #end for
    #elif str($repeat.software_cond.software) == "deeptools"
      @DEEPTOOLS_INPUT@
    #elif str($repeat.software_cond.software) == "fastp"
        #set $pattern = "report_title"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
            ln -s '$file' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
        #end for
    #elif str($repeat.software_cond.software) == "fastqc"
        @FASTQC_INPUT@
    #elif str($repeat.software_cond.software) == "featureCounts"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_prefix = os.path.join($software_dir, str($identifier))
            if grep -qw Status '$file'; then
                ln -s '$file' '${file_prefix}.summary';
            else
                echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
                cat '$file' >> '${file_prefix}.summary';
            fi &&
        #end for
    #elif str($repeat.software_cond.software) == "flexbar"
        #set $pattern = "flexible barcode and adapter removal"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "gatk"
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "varianteval"
                #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
                @LN_2_FILES@
            #elif str($repeat2.type) == "base_recalibrator"
                #set $pattern = "#:GATKTable:Arguments:Recalibration"
                @LN_2_FILES@
            #end if
        #end for
    #elif str($repeat.software_cond.software) == "hicup"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
            ln -s '${file}' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "hisat2"
        #set $pattern = "HISAT2 summary stats:"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "hicexplorer"
        #set $pattern = "Min rest. site distance"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "htseq"
        #set $pattern = "__too_low_aQual"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "kallisto"
        #set $pattern = "finding pseudoalignments for the reads"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "macs2"
        #set $pattern = "# This file is generated by MACS"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
            grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "picard"
        @PICCARD_INPUT@
    #elif str($repeat.software_cond.software) == "prokka"
        #set $pattern = "contigs:"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "pycoqc"
        #set $pattern = "\"pycoqc\":"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "qualimap"
        @QUALIMAP_INPUT@
    #elif str($repeat.software_cond.software) == "quast"
        #for $k, $file in enumerate($repeat.software_cond.input)
            #set file_dir = os.path.join($software_dir, 'file_' + str($k))
            #set file_path = os.path.join($file_dir, 'report.tsv')
            mkdir '$file_dir' &&
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "rsem"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "rseqc"
        @RSEQ_INPUT@
    #elif str($repeat.software_cond.software) == "salmon"
        @SALMON_INPUT@
    #elif str($repeat.software_cond.software) == "samblaster"
        #set $pattern = "samblaster: Version"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "samtools"
        @SAMTOOLS_INPUT@
    #elif str($repeat.software_cond.software) == "slamdunk"
        #set $pattern = "# slamdunk"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "snpeff"
        #set $pattern = "SnpEff_version"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "sortmerna"
        #set $pattern = "Minimal SW score based on E-value"
        @LN_FILES@
    #else if str($repeat.software_cond.software) == "star":
        @STAR_INPUT@
    #elif str($repeat.software_cond.software) == "tophat"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "trimmomatic"
        #set $pattern = "Trimmomatic"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "vcftools"
        @VCFTOOLS_INPUT@
    #else if str($repeat.software_cond.software) == "custom_content":
        #set $configfile = "T"
        #for $j, $file in enumerate( $repeat.software_cond.input )
            #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
            ln -s '$file' '$file_path' &&
            more $file &&
        #end for
    #end if
#end for

multiqc multiqc_WDir
--filename 'report'

#if str($title)
    --title '$title'
#end if
#if str($comment)
    --comment '$comment'
#end if

$flat
$export

#if $configfile == "T"
    --config '$multiqc_config'
#end if
    ]]></command>
    <configfiles>
        <configfile name="multiqc_config">
<![CDATA[
custom_data:
#for $i, $repeat in enumerate( $results )
    #if str($repeat.software_cond.software) == "custom_content"
    section_$i:
        file_format: 'tsv'
        section_name: '$repeat.software_cond.section_name'
        title: '$repeat.software_cond.title'
        description: '$repeat.software_cond.description'
        plot_type: '$repeat.software_cond.plot_type'
        pconfig:
            id: 'section_${i}_${repeat.software_cond.plot_type}'
            ylab: '$repeat.software_cond.ylab'
            xlab: '$repeat.software_cond.xlab'
    #end if
#end for
sp:
#for $i, $repeat in enumerate( $results )
    #if str($repeat.software_cond.software) == "custom_content"
    section_$i:
        fn: 'file_${i}_*'
    #end if
#end for
        ]]></configfile>
    </configfiles>
    <inputs>
        <repeat name="results" title="Results" min="1">
            <conditional name="software_cond">
                <param name="software" type="select" label="Which tool was used generate logs?" help="Software name">
                    <!--<option value="adapterRemoval">Adapter Removal</option>-->
                    <!--<option value="afterqc">AfterQC</option>-->
                    <option value="bamtools">Bamtools</option>
                    <!--<option value="bbmap">BBMap</option>-->
                    <option value="bcftools">Bcftools</option>
                    <!--<option value="bcl2fastq">bcl2fastq</option>-->
                    <!--<option value="biobambam2">biobambam2</option>-->
                    <!--<option value="biobloomtools">BioBloom Tools</option>-->
                    <option value="bismark">Bismark</option>
                    <!--<option value="bowtie1">Bowtie 1</option>-->
                    <option value="bowtie2">Bowtie 2</option>
                    <option value="busco">BUSCO</option>
                    <!--<option value="clusterflow">Cluster Flow</option>-->
                    <option value="cutadapt">Cutadapt/Trim Galore!</option>
                    <!--<option value="clipandmerge">ClipAndMerge</option>-->
                    <!--<option value="conpair">Conpair</option>-->
                    <!--<option value="dedup">DeDup</option>-->
                    <option value="deeptools">deepTools</option>
                    <!--<option value="disambiguate">Disambiguate</option>-->
                    <!--<option value="fastq_screen">FastQ Screen</option>-->
                    <option value="fastp">fastp</option>
                    <option value="fastqc">FastQC</option>
                    <option value="featureCounts">featureCounts</option>
                    <!--<option value="fgbio">fgbio</option>-->
                    <option value="flexbar">Flexbar</option>
                    <option value="gatk">GATK</option>
                    <!--<option value="goleft_indexcov">goleft indexcov</option>-->
                    <option value="hicexplorer">HiCExplorer</option>
                    <!--<option value="hicup">HiCUP</option>-->
                    <option value="hisat2">HISAT2</option>
                    <!--<option value="homer">HOMER</option>-->
                    <option value="htseq">HTSeq</option>
                    <!--<option value="interop">InterOp</option>-->
                    <!--<option value="jellyfish">Jellyfish</option>-->
                    <option value="kallisto">Kallisto</option>
                    <!--<option value="leehom">leeHom</option>-->
                    <option value="macs2">MACS2</option>
                    <!--<option value="methylQA">methylQA</option>-->
                    <!--<option value="mosdepth">mostdepth</option>-->
                    <!--<option value="mtnucratio">mtnucratio</option>-->
                    <!--<option value="peddy">Peddy</option>-->
                    <option value="picard">Picard</option>
                    <!--<option value="preseq">Preseq</option>-->
                    <option value="prokka">Prokka</option>
                    <option value="pycoqc">PycoQC</option>
                    <!--<option value="qorts">QoRTs</option>-->
                    <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
                    <option value="quast">QUAST</option>
                    <!--<option value="rna_seqc">RNA-SeQC</option>-->
                    <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
                    <option value="rseqc">RSeQC</option>
                    <!--<option value="salmon">Salmon</option>-->
                    <option value="samblaster">Samblaster</option>
                    <option value="samtools">Samtools</option>
                    <!--<option value="sargasso">Sargasso</option>-->
                    <!--<option value="seqyclean">SeqyClean</option>-->
                    <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
                    <!--<option value="skewer">Skewer</option>-->
                    <option value="slamdunk">Slamdunk</option>
                    <option value="snpeff">SnpEff</option>
                    <option value="sortmerna">SortMeRNA</option>
                    <option value="star">STAR</option>
                    <!--<option value="supernova">Supernova</option>-->
                    <!--<option value="theta2">THeTA2</option>-->
                    <option value="tophat">TopHat2</option>
                    <option value="trimmomatic">Trimmomatic</option>
                    <option value="vcftools">VCFTools</option>
                    <!--<option value="verifybamid">VerifyBAMID</option>-->
                    <!--Custom-->
                    <option value="custom_content">Custom Content</option>
                </param>
                <when value="bamtools">
                    <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/>
                </when>
                <when value="bcftools">
                    <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/>
                </when>
                <when value="bismark">
                    <repeat name="output" title="Bismark output" min="1">
                        <param name="type" type="select" label="Type of Bismark output?">
                            <option value="align">Alignment file</option>
                            <option value="dedup">Deduplication file</option>
                            <option value="meth_extract">Methylation file</option>
                            <option value="m_bias">m_bias file</option>
                            <option value="bam2nuc">bam2nuc file</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
                    </repeat>
                </when>
                <when value="bowtie2">
                    <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/>
                </when>
                <when value="busco">
                    <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
                </when>
                <when value="cutadapt">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/>
                </when>
                <when value="deeptools">
                    <repeat name="output" title="deepTools output" min="1">
                        <param name="type" type="select" label="deepTool used to generate the output?">
                            <option value="bamPEFragmentSize">bamPEFragmentSize</option>
                            <option value="estimateReadFiltering">estimateReadFiltering</option>
                            <option value="plotCoverageStdout">plotCoverageStdout</option>
                            <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option>
                            <option value="plotEnrichment">plotEnrichment</option>
                            <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option>
                            <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
                    </repeat>
                </when>
                <when value="fastp">
                    <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/>
                </when>
                <when value="fastqc">
                    <repeat name="output" title="FastQC output" min="1">
                        <param name="type" type="select" label="Type of FastQC output?">
                            <option value="data">Raw data</option>
                            <option value="theoretical_gc">Theorectical GC</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
                            <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
                        </param>
                    </repeat>
                </when>
                <when value="featureCounts">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
                </when>
                <when value="flexbar">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Flexbar" help="It should contain 'Flexbar - flexible barcode and adapter removal'"/>
                </when>
                <when value="gatk">
                    <repeat name="output" title="GATK output" min="1">
                        <param name="type" type="select" label="Type of GATK output?">
                            <option value="varianteval">Variant eval file</option>
                            <option value="base_recalibrator">Base recalibrator file</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
                    </repeat>
                </when>
                <when value="hicexplorer">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
                </when>
                <when value="hisat2">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
                </when>
                <when value="htseq">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>
                </when>
                <when value="kallisto">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/>
                </when>
                <when value="macs2">
                    <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
                </when>
                <when value="picard">
                    <repeat name="output" title="Picard output" min="1">
                        <param name="type" type="select" label="Type of Picard output?">
                            <option value="alignment_metrics">Alignment metrics</option>
                            <option value="basedistributionbycycle">Base distribution by cycle</option>
                            <option value="gcbias">GC bias</option>
                            <option value="hsmetrics">HS Metrics</option>
                            <option value="insertsize">Insert size</option>
                            <option value="markdups">Markdups</option>
                            <option value="oxogmetrics">Oxog metrics</option>
                            <option value="pcr_metrics">PCR metrics</option>
                            <option value="rnaseqmetrics">RNA Seq metrics</option>
                            <option value="rrbs_metrics">RRBS metrics</option>
                            <option value="wgs_metrics">WGS metrics</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
                    </repeat>
                </when>
                <when value="prokka">
                    <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
                </when>
                <when value="pycoqc">
                    <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/>
                </when>
                <when value="qualimap">
                    <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
                </when>
                <when value="quast">
                    <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/>
                </when>
                <when value="rseqc">
                    <repeat name="output" title="RSeQC output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of RSeQC output?">
                                <option value="bam_stat">BAM/SAM mapping stats</option>
                                <option value="gene_body_coverage">Gene body coverage</option>
                                <option value="infer_experiment">Infer experiment</option>
                                <option value="inner_distance">Inner distance</option>
                                <option value="junction_annotation">Junction annotation</option>
                                <option value="junction_saturation">Junction saturation</option>
                                <option value="read_distribution">Read distribution</option>
                                <option value="read_duplication_pos">Read duplication</option>
                                <option value="read_gc">Read GC</option>
                            </param>
                            <when value="bam_stat">
                                <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/>
                            </when>
                            <when value="gene_body_coverage">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage:  stats file"/>
                            </when>
                            <when value="infer_experiment">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/>
                            </when>
                            <when value="inner_distance">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/>
                            </when>
                            <when value="junction_annotation">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/>
                            </when>
                            <when value="junction_saturation">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/>
                            </when>
                            <when value="read_distribution">
                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group               Total_bases         Tag_count           Tags/Kb'"/>
                            </when>
                            <when value="read_duplication_pos">
                                <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/>
                            </when>
                            <when value="read_gc">
                                <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="samblaster">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Samblaster" help="It should contain 'samblaster: Version'"/>
                </when>
                <when value="samtools">
                    <repeat name="output" title="Samtools output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of Samtools output?">
                                <option value="stats">stats</option>
                                <option value="flagstat">flagstat</option>
                                <option value="idxstats">idxstats</option>
                                <option value="rmdup">rmdup</option>
                            </param>
                            <when value="stats">
                                <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/>
                            </when>
                            <when value="flagstat">
                                <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/>
                            </when>
                            <when value="idxstats">
                                <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/>
                            </when>
                            <when value="rmdup">
                                <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="slamdunk">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
                </when>
                <when value="snpeff">
                    <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
                </when>
                <when value="sortmerna">
                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
                </when>
                <when value="star">
                    <repeat name="output" title="STAR output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of STAR output?">
                                <option value="log">Log</option>
                                <option value="genecounts">Gene counts</option>
                            </param>
                            <when value="log">
                                <param name="input" type="data" format="txt" multiple="true" label="STAR log output"/>
                            </when>
                            <when value="genecounts">
                                <param name="input" type="data" format="tabular,tsv" multiple="true" label="STAR gene count output"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="tophat">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/>
                </when>
                <when value="trimmomatic">
                    <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/>
                </when>
                <when value="vcftools">
                    <repeat name="output" title="VCFTools output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of VCFTools output?">
                                <option value="relatedness2">relatedness2</option>
                                <option value="tstv_by_count">tstv_by_count</option>
                                <option value="tstv_by_qual">tstv_by_qual</option>
                                <option value="tstv_summary">tstv_summary</option>
                            </param>
                            <when value="relatedness2">
                                <param name="input" type="data" format="txt" multiple="true" label="VCFTools relatedness2 output"/>
                            </when>
                            <when value="tstv_by_count">
                                <param name="input" type="data" format="tabular,tsv" multiple="true" label="VCFTools TsTV count output"/>
                            </when>
                            <when value="tstv_by_qual">
                                <param name="input" type="data" format="tabular" multiple="true" label="VCFTools TsTV qual output"/>
                            </when>
                            <when value="tstv_summary">
                                <param name="input" type="data" format="txt" multiple="true" label="VCFTools TsTV summary output"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="custom_content">
                    <param argument="plot_type" label="The plot type to visualise the data with" type="select">
                        <option value="linegraph">linegraph</option>
                        <option value="bargraph">bargraph</option>
                        <option value="scatter">scatter</option>
                        <option value="generalstats">generalstats</option>
                        <option value="table">table</option>
                    </param>
                    <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header" />
                    <param argument="title" label="Title" type="text" help="Plot title" />
                    <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header" />
                    <param argument="xlab" label="X axis label" type="text" />
                    <param argument="ylab" label="Y axis label" type="text" />
                    <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/>
                </when>
            </conditional>
        </repeat>
        <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header">
            <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits">
                    <add value="," />
                    <add value=":" />
                    <add value="-" />
                    <add value="_" />
                    <add value=" " />
                    <add value="." />
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z,: _.-]+</validator>
        </param>
        <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report">
            <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits">
                    <add value="," />
                    <add value=":" />
                    <add value="-" />
                    <add value="_" />
                    <add value=" " />
                    <add value="." />
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z,: _.-]+</validator>
        </param>
        <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
        <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
        <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
    </inputs>
    <outputs>
        <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
        <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
            <filter>saveLog</filter>
        </data>
        <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
            <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
        </collection>
        <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
            <filter>export</filter>
        </collection>
    </outputs>
    <tests>
        <!--Test 01-->
        <test expect_num_outputs="4">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="cutadapt" />
                    <param name="input" value="cutadapt.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastp" />
                    <param name="input" value="fastp1.json.txt,fastp2.json.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastqc" />
                    <repeat name="output">
                        <param name="type" value="data"/>
                        <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="flexbar" />
                    <param name="input" value="flexbar.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="slamdunk" />
                    <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="sortmerna" />
                    <param name="input" value="sortmerna.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="trimmomatic" />
                    <param name="input" value="trimmomatic.txt" />
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <param name="saveLog" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report" />
                    <has_text text="Commment for the report" />
                    <has_text text="cutadapt_trimmed_sequences_plot" />
                    <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                    <has_text text="fastqc_seq_heatmap_key_t" />
                    <has_text text="flexbar_plot" />
                    <has_text text="a tool to analyze SLAMSeq data" />
                    <has_text text="sortmerna-detailed-plot" />
                    <has_text text="trimmomatic_plot" />
                </assert_contents>
            </output>
            <output name="log">
                <assert_contents>
                    <has_text_matching expression="\[INFO   \]  MultiQC complete$"/>
                </assert_contents>
            </output>
            <output_collection name="stats" type="list" count="10">
                <expand macro="element_assert" name="cutadapt" columns="9" lines="2" text="dataset_33"/>
                <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/>
                <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/>
                <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/>
                <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/>
                <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
                <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
                <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/>
                <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/>
                <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/>
            </output_collection>
            <output_collection name="plots" type="list" count="29"/>
        </test>
        <!--Test 02-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bismark" />
                    <repeat name="output">
                        <param name="type" value="align"/>
                        <param name="input" value="bismark.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bowtie2" />
                    <param name="input" value="bowtie2_1.txt,bowtie2_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="hisat2" />
                    <param name="input" value="hisat2_1.txt,hisat2_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="hicexplorer" />
                    <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="kallisto" />
                    <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="macs2" />
                    <param name="input" value="macs_1.txt,macs_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="star" />
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="log"/>
                            <param name="input" value="star_log.txt" />
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="genecounts"/>
                            <param name="input" value="star_counts.txt" />
                        </conditional>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="tophat" />
                    <param name="input" value="tophat.txt" />
                </conditional>
            </repeat>
            <param name="saveLog" value="false"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="bismark-alignment" />
                    <has_text text="bowtie2_se_plot" />
                    <has_text text="hisat2_se_plot" />
                    <has_text text="kallisto_alignment" />
                    <has_text text="MACS2" />
                    <has_text text="star_alignment_plot" />
                    <has_text text="tophat_alignment" />
                    <has_text text="hicexplorer" />
                    <has_text text="hicexplorer1_log_1" />
                </assert_contents>
            </output>
            <output_collection name="stats" type="list" count="11">
                <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/>
                <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/>
                <expand macro="element_assert" name="cutadapt" columns="9" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/>
                <expand macro="element_assert" name="general_stats" columns="22"  lines="19" text="treat2"/>
                <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
                <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/>
                <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/>
                <expand macro="element_assert" name="macs" columns="12" lines="3" text="treat2"/>
                <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/>
                <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/>
                <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/>
            </output_collection>
        </test>
        <!--Test 03-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bamtools" />
                    <param name="input" value="bamtools.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bcftools" />
                    <param name="input" value="bcftools.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="busco" />
                    <param name="input" value="busco.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="deeptools" />
                    <repeat name="output">
                        <param name="type" value="bamPEFragmentSize"/>
                        <param name="input" value="deeptools_bamPEFragmentSize.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="estimateReadFiltering"/>
                        <param name="input" value="deeptools_estimateReadFiltering.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="plotCoverageStdout"/>
                        <param name="input" value="deeptools_plotCoverageStdout.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="plotCoverageOutRawCounts"/>
                        <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="plotEnrichment"/>
                        <param name="input" value="deeptools_plotEnrichment.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="plotFingerprintOutRawCounts"/>
                        <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="featureCounts" />
                    <param name="input" value="featureCounts.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="gatk" />
                    <repeat name="output">
                        <param name="type" value="base_recalibrator"/>
                        <param name="input" value="gatk_BaseRecalibrator.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="varianteval"/>
                        <param name="input" value="gatk_varianteval.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="htseq" />
                    <param name="input" value="htseq.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="picard" />
                    <repeat name="output">
                        <param name="type" value="gcbias"/>
                        <param name="input" value="picard_collectGcBias.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="insertsize"/>
                        <param name="input" value="picard_CollectInsertSizeMetrics.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="markdups"/>
                        <param name="input" value="picard_MarkDuplicates.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="basedistributionbycycle"/>
                        <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="rnaseqmetrics"/>
                        <param name="input" value="picard_CollectRnaSeqMetrics.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="alignment_metrics"/>
                        <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="prokka" />
                    <param name="input" value="prokka_1.txt,prokka_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="qualimap" />
                    <param name="input" value="genome_results.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="quast" />
                    <param name="input" value="quast.tsv" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="rseqc" />
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="read_gc"/>
                            <param name="input" value="rseqc.txt"/>
                        </conditional>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="samblaster" />
                    <param name="input" value="samblaster.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="samtools" />
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="stats"/>
                            <param name="input" value="samtools_stats.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="flagstat"/>
                            <param name="input" value="samtools_flagstat.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="idxstats"/>
                            <param name="input" value="samtools_idxstats.txt"/>
                        </conditional>
                    </repeat>
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="snpeff" />
                    <param name="input" value="snpeff.csv" ftype="csv" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="vcftools" />
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="tstv_by_qual"/>
                            <param name="input" value="vcftools.txt"/>
                        </conditional>
                    </repeat>
                    <param name="input" value="vcftools.txt" />
                </conditional>
            </repeat>
            <output name="html_report">
                <assert_contents>
                    <has_text text="bamtools-stats" />
                    <has_text text="bcftools_stats_indel-lengths" />
                    <has_text text="busco-lineage-fungi_odb9" />
                    <has_text text="deeptools" />
                    <has_text text="featureCounts_assignment_plot" />
                    <has_text text="gatk_varianteval_variant_plot" />
                    <has_text text="htseq_assignment_plot" />
                    <has_text text="picard_alignment_readlength" />
                    <has_text text="picard-rna-assignment" />
                    <has_text text="picard-markduplicates" />
                    <has_text text="picard-insertsize" />
                    <has_text text="picard-gcbias" />
                    <has_text text="prokka_plot" />
                    <has_text text="qualimap" />
                    <has_text text="samblaster_duplicates" />
                    <has_text text="quast-stats" />
                    <has_text text="samtools-flagstat-dp" />
                    <has_text text="snpeff" />
                </assert_contents>
            </output>
            <output_collection name="stats" type="list" count="21">
                <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/>
                <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/>
                <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/>
                <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/>
                <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/>
                <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/>
                <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/>
                <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
                <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/>
                <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
                <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/>
                <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/>
                <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/>
                <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/>
                <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/>
                <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/>
                <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt">
                    <has_text text="samtools_flagstat" />
                    <has_text text="mapped_passed" />
                    <has_text text="20689039" />
                </expand>
                <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/>
                <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/>
                <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/>
                <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/>
            </output_collection>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="custom_content" />
                    <param name="cc_select" value="manual" />
                    <param name="plot_type" value="linegraph" />
                    <param name="section_name" value="BPC" />
                    <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)" />
                    <param name="xlab" value="Retention Time" />
                    <param name="ylab" value="Base Peak Intensity" />
                    <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" />
                </conditional>
            </repeat>
            <output name="html_report" ftype="html">
                <assert_contents>
                    <has_size value="1110578" delta="500" />
                </assert_contents>
            </output>
	        <output_collection name="stats" type="list" count="1"/>
        </test>
        <!--Test 05-->
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastqc" />
                    <repeat name="output">
                        <param name="type" value="data"/>
                        <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report" />
                    <has_text text="Commment for the report" />
                    <has_text text="fastqc_seq_heatmap_key_t" />
                </assert_contents>
            </output>
	        <output_collection name="stats" type="list" count="3">
                <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/>
                <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/>
                <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/>
            </output_collection>
            <output_collection name="plots" type="list" count="7">
                <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
            </output_collection>
        </test>
        <!--Test 06-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="pycoqc" />
                    <param name="input" value="pycoqc.json"/>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <!-- <param name="flat" value="true"/> -->
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report" />
                    <has_text text="Commment for the report" />
                    <has_text text="General Statistics" />
                    <has_text text="pycoqc_count_plot" />
                    <has_text text="pycoqc_read_len_plot" />
                    <has_text text="pycoqc_read_qual_plot" />
                </assert_contents>
            </output>
	    <output_collection name="stats" type="list" count="2"/>
        </test>
        <!--Test 07-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="rseqc" />
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="junction_annotation"/>
                            <param name="input" value="junction_annotation.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="junction_saturation"/>
                            <param name="input" value="junction_saturation.txt"/>
                        </conditional>
                    </repeat>
                </conditional>
            </repeat>
            <param name="title" value="RSEQC report"/>
            <!-- <param name="flat" value="true"/> -->
            <output name="html_report">
                <assert_contents>
                    <has_text text="RSEQC report" />
                    <has_text text="Junction Annotation" />
                    <has_text text="Junction Saturation" />
                </assert_contents>
            </output>
	        <output_collection name="stats" type="list" count="2"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.

**Inputs**

MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC

----

The first integration of this tool was made by
`@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_.
It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btw354</citation>
    </citations>
</tool>