comparison multiqc.xml @ 13:e17597fc06fb draft

Updated xml file from github

12:e95b3d2c3dc0

<tool id="multiqc" name="multiqc" version="1.0.0.0">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <requirements>
       <requirement type="package" version="1.0.0">multiqc</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        mkdir multiqc_WDir;
        
        #for $i, $repeat in enumerate( $results )
            mkdir multiqc_WDir/${repeat.software}_${i};

            #if str($repeat.software) == "fastqc":
                ## Searches for files named "fastqc_data.txt"
                #for $k, $file in enumerate($repeat.input_file):
                    mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};
                    ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt;
                #end for           
            #else if str($repeat.software) == "tophat":
                ## Searches for files ending in "align_summary.txt"
                #for $file in $repeat.input_file:
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}align_summary.txt';
                #end for
            #else if str($repeat.software) == "bowtie2":
                ## Searches for files containing 'reads; of these;'
                #for $file in $repeat.input_file:
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';
                #end for
            #else if str($repeat.software) == "cutadapt":
                ## Searches for files containing 'This is cutadapt'
                #for $file in $repeat.input_file:
                    cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';
                    ## replace header for old cutadapt release
                    sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';               
                #end for
            #else if str($repeat.software) == "featurecounts":
                ## Checks for files ending in '.summary'
                #for $k, $file in enumerate($repeat.input_file):
                    mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/file_${k}/${file.display_name}.summary';
                #end for
            #else if str($repeat.software) == "bismark":
                ## Checks for files ending in _SE_report.txt
                #for $file in $repeat.input_file
                    ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_SE_report.txt';
                #end for
            #else if str($repeat.software) == "samtools":
                ## Checks for files containing 'This file was produced by samtools stats'
                #for $file in $repeat.input_file
                    ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
                #end for
            #else if str($repeat.software) == "picard":
                #for $file in $repeat.input_file
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
                #end for 
            #else if str($repeat.software) == "samtools_idxstats":
                ## Checks for files containing "idxstats" in the name
                #for $file in $repeat.input_file
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_idxstats.txt';
                #end for 
            #else if str($repeat.software) == "htseq":
                ## Checks for files containing "__too_low_aQual"
                #for $file in $repeat.input_file
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
                #end for 
            #else if str($repeat.software) == "rnastar_log":
                ## Checks for files named Log.final.out
                #for $k, $file in enumerate($repeat.input_file):
                    mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/Log.final.out';
                #end for 
            #else if str($repeat.software) == "rnastar_counts":
                ## Checks for files named ReadsPerGene.out.tab
                #for $k, $file in enumerate($repeat.input_file):
                    mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
                    ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/ReadsPerGene.out.tab';
                #end for 
            #end if
        #end for

        multiqc multiqc_WDir; 
       
    </command>
    <inputs>
        <repeat name="results" title="Results" min="1">
            <param name="software" type="select" label="Software name" help="Which tool was used generate logs?">
                <option value="fastqc">FastQC</option>
                <option value="cutadapt">Cutadapt/Trim Galore!</option>
                <option value="tophat">Tophat2</option>
                <option value="featurecounts">FeatureCounts (Summary file)</option>
                <option value="samtools">Samtools (Stats, Flagstat)</option>
                <option value="samtools_idxstats">Samtools (Idxstats)</option>
                <option value="picard">Picard</option>
                <option value="bismark">Bismark</option>
                <option value="bowtie2">Bowtie2</option>
                <option value="htseq">HTSeq-Count</option>
                <option value="rnastar_log">RNA STAR (log)</option>
                <option value="rnastar_counts">RNA STAR (reads per gene)</option>
            </param>
            <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/>
            <param name="saveLog" type="boolean" checked="false" label="Save log file" help="Save the multiQC log file to the history. This is mostly useful for debugging purposes."/>
        </repeat>
    </inputs>
    <outputs>
        <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
        <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
            <filter>saveLog is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <repeat name="results">
                <param name="software" value="fastqc" />
                <param name="input_file" value="fastqc_data.txt" />
            </repeat>
            <param name="saveLog" value="True"/>
            <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/>
            <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/>     
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="fastqc" />
                <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
            </repeat>
            <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="cutadapt" />
                <param name="input_file" value="cutadapt.txt" />
            </repeat>
            <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="tophat" />
                <param name="input_file" value="tophat_data.txt" />
            </repeat>
            <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="bowtie2" />
                <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" />
            </repeat>
            <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="featurecounts" />
                <param name="input_file" value="featurecounts_data.txt" />
            </repeat>
            <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="picard" />
                <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" />
            </repeat>
            <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="htseq" />
                <param name="input_file" value="htseq_data.txt" />
            </repeat>
            <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="rnastar_log" />
                <param name="input_file" value="rnastar_log.txt" />
            </repeat>
            <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="rnastar_counts" />
                <param name="input_file" value="rnastar_counts.txt" />
            </repeat>
            <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="bismark" />
                <param name="input_file" value="bismark_data.txt" />
            </repeat>
            <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="samtools" />
                <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
            </repeat>
            <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="samtools_idxstats" />
                <param name="input_file" value="samtools_idxstats.txt" />
            </repeat>
            <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <repeat name="results">
                <param name="software" value="fastqc" />
                <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="cutadapt" />
                <param name="input_file" value="cutadapt.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="tophat" />
                <param name="input_file" value="tophat_data.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="featurecounts" />
                <param name="input_file" value="featurecounts_data.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="picard" />
                <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="bismark" />
                <param name="input_file" value="bismark_data.txt" />
            </repeat>
            <repeat name="results">
                <param name="software" value="samtools" />
                <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
            </repeat>
            <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/>
        </test>
    </tests>

    <help>
**What it does**

MultiQC 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 the following Galaxy tools produce logs that can used with MultiQC. There are:

- Fastqc
- Cutadapt / Trim Galore!
- Tophat2
- FeatureCounts
- Samtools (stats, flagstat, dxstats)
- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)
- Bismark (Alignment report file)
- Bowtie2 (Metrics file)
- HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)
- RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)

----

**Integrated by**

Cyril Monjeaud and Yvan Le Bras

`EnginesOn &lt;http://engineson.fr/&gt;`_ and Rennes GenOuest Bio-informatics Core Facility

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btw354</citation>
    </citations>
</tool>

13:e17597fc06fb

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  <div itemprop="text" class="blob-wrapper data type-xml">
      <table class="highlight tab-size js-file-line-container" data-tab-size="8">
      <tr>
        <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
        <td id="LC1" class="blob-code blob-code-inner js-file-line">&lt;<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@.0<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
        <td id="LC2" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">description</span>&gt;aggregate results from bioinformatics analyses into a single report&lt;/<span class="pl-ent">description</span>&gt;</td>
      </tr>
      <tr>
        <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
        <td id="LC3" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">macros</span>&gt;</td>
      </tr>
      <tr>
        <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
        <td id="LC4" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">token</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@<span class="pl-pds">&quot;</span></span>&gt;1.0.0&lt;/<span class="pl-ent">token</span>&gt;</td>
      </tr>
      <tr>
        <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
        <td id="LC5" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">macros</span>&gt;</td>
      </tr>
      <tr>
        <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
        <td id="LC6" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">requirements</span>&gt;</td>
      </tr>
      <tr>
        <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
        <td id="LC7" class="blob-code blob-code-inner js-file-line">       &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@<span class="pl-pds">&quot;</span></span>&gt;multiqc&lt;/<span class="pl-ent">requirement</span>&gt;</td>
      </tr>
      <tr>
        <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
        <td id="LC8" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">requirements</span>&gt;</td>
      </tr>
      <tr>
        <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
        <td id="LC9" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">version_command</span>&gt;@WRAPPER_VERSION@&lt;/<span class="pl-ent">version_command</span>&gt;</td>
      </tr>
      <tr>
        <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
        <td id="LC10" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">command</span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>aggressive<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
        <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">&lt;![CDATA[</span></span></td>
      </tr>
      <tr>
        <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
        <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s">mkdir multiqc_WDir &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
        <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
        <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#for $i, $repeat in enumerate( $results )</span></td>
      </tr>
      <tr>
        <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
        <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    mkdir multiqc_WDir/${repeat.software}_${i} &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
        <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
        <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #if str($repeat.software) == &quot;fastqc&quot;:</span></td>
      </tr>
      <tr>
        <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
        <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Searches for files named &quot;fastqc_data.txt&quot;</span></td>
      </tr>
      <tr>
        <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
        <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $k, $file in enumerate($repeat.input_file):</span></td>
      </tr>
      <tr>
        <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
        <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
        <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
        <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
        <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;tophat&quot;:</span></td>
      </tr>
      <tr>
        <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
        <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Searches for files ending in &quot;align_summary.txt&quot;</span></td>
      </tr>
      <tr>
        <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
        <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file:</span></td>
      </tr>
      <tr>
        <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
        <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
        <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
        <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;bowtie2&quot;:</span></td>
      </tr>
      <tr>
        <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
        <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Searches for files containing &#39;reads; of these;&#39;</span></td>
      </tr>
      <tr>
        <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
        <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file:</span></td>
      </tr>
      <tr>
        <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
        <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
        <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
        <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;cutadapt&quot;:</span></td>
      </tr>
      <tr>
        <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
        <td id="LC34" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Searches for files containing &#39;This is cutadapt&#39;</span></td>
      </tr>
      <tr>
        <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
        <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file:</span></td>
      </tr>
      <tr>
        <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
        <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            cat &#39;${file}&#39; &gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
        <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ## replace header for old cutadapt release</span></td>
      </tr>
      <tr>
        <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
        <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            sed -i .old &#39;s/You are running/This is/&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
        <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
        <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;featurecounts&quot;:</span></td>
      </tr>
      <tr>
        <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
        <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files ending in &#39;.summary&#39;</span></td>
      </tr>
      <tr>
        <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
        <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
        <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            #if $file.metadata.column_names and $file.metadata.column_names.find(&#39;,&#39;) != -1</span></td>
      </tr>
      <tr>
        <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
        <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-s">                echo &#39;$file.metadata.column_names.replace(&#39;,&#39;,&#39;\t&#39;).replace(&#39;__ob__u&#39;,&#39;&#39;).replace(&#39;u__sq__&#39;,&#39;&#39;).replace(&#39;__sq__&#39;,&#39;&#39;).replace(&#39;__cb__&#39;,&#39;&#39;)&#39; &gt;&gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
        <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-s">                cat &#39;$file&#39; &gt;&gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
        <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            #else</span></td>
      </tr>
      <tr>
        <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
        <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-s">                ln -s &#39;$file&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
        <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            #end if</span></td>
      </tr>
      <tr>
        <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
        <td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
        <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;bismark&quot;:</span></td>
      </tr>
      <tr>
        <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
        <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files ending in _SE_report.txt</span></td>
      </tr>
      <tr>
        <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
        <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
        <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s ${file} &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
        <td id="LC54" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
        <td id="LC55" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;samtools&quot;:</span></td>
      </tr>
      <tr>
        <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
        <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files containing &#39;This file was produced by samtools stats&#39;</span></td>
      </tr>
      <tr>
        <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
        <td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
        <td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s ${file} &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
        <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
        <td id="LC60" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;picard&quot;:</span></td>
      </tr>
      <tr>
        <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
        <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
        <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
        <td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
        <td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;samtools_idxstats&quot;:</span></td>
      </tr>
      <tr>
        <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
        <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files containing &quot;idxstats&quot; in the name</span></td>
      </tr>
      <tr>
        <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
        <td id="LC66" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
        <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
        <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
        <td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;htseq&quot;:</span></td>
      </tr>
      <tr>
        <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
        <td id="LC70" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files containing &quot;__too_low_aQual&quot;</span></td>
      </tr>
      <tr>
        <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
        <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $file in $repeat.input_file</span></td>
      </tr>
      <tr>
        <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
        <td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
        <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
        <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;rnastar_log&quot;:</span></td>
      </tr>
      <tr>
        <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
        <td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files named Log.final.out</span></td>
      </tr>
      <tr>
        <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
        <td id="LC76" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $k, $file in enumerate($repeat.input_file):</span></td>
      </tr>
      <tr>
        <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
        <td id="LC77" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            mkdir &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
        <td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
        <td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
        <td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #else if str($repeat.software) == &quot;rnastar_counts&quot;:</span></td>
      </tr>
      <tr>
        <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
        <td id="LC81" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        ## Checks for files named ReadsPerGene.out.tab</span></td>
      </tr>
      <tr>
        <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
        <td id="LC82" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #for $k, $file in enumerate($repeat.input_file):</span></td>
      </tr>
      <tr>
        <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
        <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            mkdir &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
        <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-s">            ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab&#39; &amp;&amp;</span></td>
      </tr>
      <tr>
        <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
        <td id="LC85" class="blob-code blob-code-inner js-file-line"><span class="pl-s">        #end for</span></td>
      </tr>
      <tr>
        <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
        <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    #end if</span></td>
      </tr>
      <tr>
        <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
        <td id="LC87" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#end for</span></td>
      </tr>
      <tr>
        <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
        <td id="LC88" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
        <td id="LC89" class="blob-code blob-code-inner js-file-line"><span class="pl-s">multiqc multiqc_WDir</span></td>
      </tr>
      <tr>
        <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
        <td id="LC90" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    <span class="pl-pds">]]&gt;</span></span>&lt;/<span class="pl-ent">command</span>&gt;</td>
      </tr>
      <tr>
        <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
        <td id="LC91" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">inputs</span>&gt;</td>
      </tr>
      <tr>
        <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
        <td id="LC92" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span> <span class="pl-e">title</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Results<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
        <td id="LC93" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Software name<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Which tool was used generate logs?<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
        <td id="LC94" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span>&gt;FastQC&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
        <td id="LC95" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span>&gt;Cutadapt/Trim Galore!&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
        <td id="LC96" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span>&gt;Tophat2&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
        <td id="LC97" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span>&gt;FeatureCounts (Summary file)&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
        <td id="LC98" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span>&gt;Samtools (Stats, Flagstat)&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
        <td id="LC99" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats<span class="pl-pds">&quot;</span></span>&gt;Samtools (Idxstats)&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
        <td id="LC100" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span>&gt;Picard&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
        <td id="LC101" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span>&gt;Bismark&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
        <td id="LC102" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2<span class="pl-pds">&quot;</span></span>&gt;Bowtie2&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
        <td id="LC103" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq<span class="pl-pds">&quot;</span></span>&gt;HTSeq-Count&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
        <td id="LC104" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log<span class="pl-pds">&quot;</span></span>&gt;RNA STAR (log)&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
        <td id="LC105" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts<span class="pl-pds">&quot;</span></span>&gt;RNA STAR (reads per gene)&lt;/<span class="pl-ent">option</span>&gt;</td>
      </tr>
      <tr>
        <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
        <td id="LC106" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">param</span>&gt;</td>
      </tr>
      <tr>
        <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
        <td id="LC107" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>txt, tabular<span class="pl-pds">&quot;</span></span> <span class="pl-e">multiple</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Result file<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Select input datasets<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
        <td id="LC108" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
        <td id="LC109" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>saveLog<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>boolean<span class="pl-pds">&quot;</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>false<span class="pl-pds">&quot;</span></span> <span class="pl-e">checked</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>false<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Save log file<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Save the multiQC log file to the history. This is mostly useful for debugging purposes.<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
        <td id="LC110" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">inputs</span>&gt;</td>
      </tr>
      <tr>
        <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
        <td id="LC111" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">outputs</span>&gt;</td>
      </tr>
      <tr>
        <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
        <td id="LC112" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html<span class="pl-pds">&quot;</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc_report.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>${tool.name} on ${on_string}: Webpage<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
        <td id="LC113" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>txt<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>text_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc_data/multiqc.log<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>${tool.name} on ${on_string}: Log<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
        <td id="LC114" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">filter</span>&gt;saveLog&lt;/<span class="pl-ent">filter</span>&gt;</td>
      </tr>
      <tr>
        <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
        <td id="LC115" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">data</span>&gt;</td>
      </tr>
      <tr>
        <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
        <td id="LC116" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">outputs</span>&gt;</td>
      </tr>
      <tr>
        <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
        <td id="LC117" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">tests</span>&gt;</td>
      </tr>
      <tr>
        <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
        <td id="LC118" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
        <td id="LC119" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
        <td id="LC120" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
        <td id="LC121" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
        <td id="LC122" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
        <td id="LC123" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>saveLog<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
        <td id="LC124" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_fastqc.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
        <td id="LC125" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>text_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>log_fastqc.txt<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
        <td id="LC126" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
        <td id="LC127" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
        <td id="LC128" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
        <td id="LC129" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
        <td id="LC130" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
        <td id="LC131" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
        <td id="LC132" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_fastqc_2.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
        <td id="LC133" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
        <td id="LC134" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
        <td id="LC135" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
        <td id="LC136" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
        <td id="LC137" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
        <td id="LC138" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
        <td id="LC139" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_cutadapt.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
        <td id="LC140" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
        <td id="LC141" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
        <td id="LC142" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
        <td id="LC143" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
        <td id="LC144" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
        <td id="LC145" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
        <td id="LC146" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_tophat.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
        <td id="LC147" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
        <td id="LC148" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
        <td id="LC149" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
        <td id="LC150" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
        <td id="LC151" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2SE1.txt,bowtie2SE2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
        <td id="LC152" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
        <td id="LC153" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_bowtie2SE.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
        <td id="LC154" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
        <td id="LC155" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
        <td id="LC156" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
        <td id="LC157" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
        <td id="LC158" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
        <td id="LC159" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
        <td id="LC160" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_featurecounts.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
        <td id="LC161" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
        <td id="LC162" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
        <td id="LC163" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
        <td id="LC164" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
        <td id="LC165" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
        <td id="LC166" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
        <td id="LC167" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_picard.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>10000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
        <td id="LC168" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
        <td id="LC169" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
        <td id="LC170" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
        <td id="LC171" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
        <td id="LC172" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
        <td id="LC173" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
        <td id="LC174" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_htseq.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
        <td id="LC175" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
        <td id="LC176" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
        <td id="LC177" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
        <td id="LC178" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
        <td id="LC179" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
        <td id="LC180" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
        <td id="LC181" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_rnastar_log.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
        <td id="LC182" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
        <td id="LC183" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
        <td id="LC184" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
        <td id="LC185" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
        <td id="LC186" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
        <td id="LC187" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
        <td id="LC188" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_rnastar_counts.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
        <td id="LC189" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
        <td id="LC190" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
        <td id="LC191" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
        <td id="LC192" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
        <td id="LC193" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
        <td id="LC194" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
        <td id="LC195" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_bismark.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
        <td id="LC196" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
        <td id="LC197" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
        <td id="LC198" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
        <td id="LC199" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
        <td id="LC200" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
        <td id="LC201" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
        <td id="LC202" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_samtools.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
        <td id="LC203" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
        <td id="LC204" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
        <td id="LC205" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
        <td id="LC206" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
        <td id="LC207" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
        <td id="LC208" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
        <td id="LC209" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_samtools_idxstats.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
        <td id="LC210" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
        <td id="LC211" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
        <td id="LC212" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
        <td id="LC213" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
        <td id="LC214" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
        <td id="LC215" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
        <td id="LC216" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
        <td id="LC217" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
        <td id="LC218" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
        <td id="LC219" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
        <td id="LC220" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
        <td id="LC221" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
        <td id="LC222" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
        <td id="LC223" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
        <td id="LC224" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
        <td id="LC225" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
        <td id="LC226" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
        <td id="LC227" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
        <td id="LC228" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
        <td id="LC229" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
        <td id="LC230" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
        <td id="LC231" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
        <td id="LC232" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
        <td id="LC233" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
        <td id="LC234" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
        <td id="LC235" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
        <td id="LC236" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
      </tr>
      <tr>
        <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
        <td id="LC237" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
        <td id="LC238" class="blob-code blob-code-inner js-file-line">                &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
      </tr>
      <tr>
        <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
        <td id="LC239" class="blob-code blob-code-inner js-file-line">            &lt;/<span class="pl-ent">repeat</span>&gt;</td>
      </tr>
      <tr>
        <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
        <td id="LC240" class="blob-code blob-code-inner js-file-line">            &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_all.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>5000<span class="pl-pds">&quot;</span></span>/&gt;</td>
      </tr>
      <tr>
        <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
        <td id="LC241" class="blob-code blob-code-inner js-file-line">        &lt;/<span class="pl-ent">test</span>&gt;</td>
      </tr>
      <tr>
        <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
        <td id="LC242" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">tests</span>&gt;</td>
      </tr>
      <tr>
        <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
        <td id="LC243" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
        <td id="LC244" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">help</span>&gt;<span class="pl-s"><span class="pl-pds">&lt;![CDATA[</span></span></td>
      </tr>
      <tr>
        <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
        <td id="LC245" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**What it does**</span></td>
      </tr>
      <tr>
        <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
        <td id="LC246" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
        <td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-s">MultiQC 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&#39;s a general use tool, perfect for summarizing the output from numerous bioinformatics tools.</span></td>
      </tr>
      <tr>
        <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
        <td id="LC248" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
        <td id="LC249" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Inputs**</span></td>
      </tr>
      <tr>
        <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
        <td id="LC250" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
        <td id="LC251" class="blob-code blob-code-inner js-file-line"><span class="pl-s">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 the following Galaxy tools produce logs that can used with MultiQC. There are:</span></td>
      </tr>
      <tr>
        <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
        <td id="LC252" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
        <td id="LC253" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Fastqc</span></td>
      </tr>
      <tr>
        <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
        <td id="LC254" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Cutadapt / Trim Galore!</span></td>
      </tr>
      <tr>
        <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
        <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Tophat2</span></td>
      </tr>
      <tr>
        <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
        <td id="LC256" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- FeatureCounts (summary file with the column header in the first line or as metadata)</span></td>
      </tr>
      <tr>
        <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
        <td id="LC257" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Samtools (stats, flagstat, dxstats)</span></td>
      </tr>
      <tr>
        <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
        <td id="LC258" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)</span></td>
      </tr>
      <tr>
        <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
        <td id="LC259" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bismark (Alignment report file)</span></td>
      </tr>
      <tr>
        <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
        <td id="LC260" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bowtie2 (Metrics file)</span></td>
      </tr>
      <tr>
        <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
        <td id="LC261" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- HTSeq-count (&quot;no feature&quot; file; although the &quot;Assigned&quot; metric is always 0)</span></td>
      </tr>
      <tr>
        <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
        <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)</span></td>
      </tr>
      <tr>
        <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
        <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
        <td id="LC264" class="blob-code blob-code-inner js-file-line"><span class="pl-s">----</span></td>
      </tr>
      <tr>
        <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
        <td id="LC265" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
        <td id="LC266" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Integrated by**</span></td>
      </tr>
      <tr>
        <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
        <td id="LC267" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
        <td id="LC268" class="blob-code blob-code-inner js-file-line"><span class="pl-s">Cyril Monjeaud and Yvan Le Bras</span></td>
      </tr>
      <tr>
        <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
        <td id="LC269" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
        <td id="LC270" class="blob-code blob-code-inner js-file-line"><span class="pl-s">`EnginesOn &amp;lt;http://engineson.fr/&amp;gt;`_ and Rennes GenOuest Bio-informatics Core Facility</span></td>
      </tr>
      <tr>
        <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
        <td id="LC271" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
      </tr>
      <tr>
        <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
        <td id="LC272" class="blob-code blob-code-inner js-file-line"><span class="pl-s">    <span class="pl-pds">]]&gt;</span></span>&lt;/<span class="pl-ent">help</span>&gt;</td>
      </tr>
      <tr>
        <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
        <td id="LC273" class="blob-code blob-code-inner js-file-line">    &lt;<span class="pl-ent">citations</span>&gt;</td>
      </tr>
      <tr>
        <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
        <td id="LC274" class="blob-code blob-code-inner js-file-line">        &lt;<span class="pl-ent">citation</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>doi<span class="pl-pds">&quot;</span></span>&gt;10.1093/bioinformatics/btw354&lt;/<span class="pl-ent">citation</span>&gt;</td>
      </tr>
      <tr>
        <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
        <td id="LC275" class="blob-code blob-code-inner js-file-line">    &lt;/<span class="pl-ent">citations</span>&gt;</td>
      </tr>
      <tr>
        <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
        <td id="LC276" class="blob-code blob-code-inner js-file-line">&lt;/<span class="pl-ent">tool</span>&gt;</td>
      </tr>
</table>

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