Mercurial > repos > engineson > multiqc
changeset 15:d6579f50e622 draft
Uploaded
author | engineson |
---|---|
date | Mon, 24 Jul 2017 08:42:27 -0400 |
parents | 784165ccd3c1 |
children | 5e4080791d90 |
files | multiqc.xml |
diffstat | 1 files changed, 265 insertions(+), 1615 deletions(-) [+] |
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--- a/multiqc.xml Fri Jul 07 08:00:39 2017 -0400 +++ b/multiqc.xml Mon Jul 24 08:42:27 2017 -0400 @@ -1,1626 +1,276 @@ - - - - - - -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - <link rel="dns-prefetch" href="https://assets-cdn.github.com"> - <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> - <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> - <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> - - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-e04a23d39bf81b7db3c635177756ef51bc171feb440be9e174933c6eb56382da.css" media="all" rel="stylesheet" /> - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-caabe7e9677dbaa4c88db92fcc52ed61b0def1a9d2e3d3ab196c0a5c81d20d04.css" media="all" rel="stylesheet" /> - 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277 lines (263 sloc) - <span class="file-info-divider"></span> - 13.7 KB - </div> -</div> - - + #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}/${file.element_identifier}align_summary.txt' && + #end for + #else if str($repeat.software) == "bowtie2": + ## Searches for files containing 'reads; of these;' + #for $file in $repeat.input_file: + ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && + #end for + #else if str($repeat.software) == "cutadapt": + ## Searches for files containing 'This is cutadapt' + #for $file in $repeat.input_file: + cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && + ## replace header for old cutadapt release + sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && + #end for + #else if str($repeat.software) == "featurecounts": + ## Checks for files ending in '.summary' + #for $file in $repeat.input_file + #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 + echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && + cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && + #else + ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && + #end if + #end for + #else if str($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.element_identifier}_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.element_identifier}' && + #end for + #else if str($repeat.software) == "picard": + #for $file in $repeat.input_file + ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && + #end for + #else if str($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}/${file.element_identifier}_idxstats.txt' && + #end for + #else if str($repeat.software) == "htseq": + ## Checks for files containing "__too_low_aQual" + #for $file in $repeat.input_file + ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && + #end for + #else if str($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}/${file.element_identifier}' && + ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' && + #end for + #else if str($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}/${file.element_identifier}' && + ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' && + #end for + #end if +#end for - <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"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@.0<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">description</span>>aggregate results from bioinformatics analyses into a single report</<span class="pl-ent">description</span>></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"> <<span class="pl-ent">macros</span>></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"> <<span class="pl-ent">token</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>1.0.0</<span class="pl-ent">token</span>></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"> </<span class="pl-ent">macros</span>></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"> <<span class="pl-ent">requirements</span>></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"> <<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>package<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>multiqc</<span class="pl-ent">requirement</span>></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"> </<span class="pl-ent">requirements</span>></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"> <<span class="pl-ent">version_command</span>>@WRAPPER_VERSION@</<span class="pl-ent">version_command</span>></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"> <<span class="pl-ent">command</span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">"</span>aggressive<span class="pl-pds">"</span></span>></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"><![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 &&</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}_${i} &&</span></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if str($repeat.software) == "fastqc":</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 "fastqc_data.txt"</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_${k} &&</span></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &&</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) == "tophat":</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 "align_summary.txt"</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 $repeat.input_file:</span></td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' &&</span></td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bowtie2":</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 'reads; of these;'</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 $repeat.input_file:</span></td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "cutadapt":</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 'This is cutadapt'</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 $repeat.input_file:</span></td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## replace header for old cutadapt release</span></td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</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) == "featurecounts":</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 '.summary'</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 $file.metadata.column_names.find(',') != -1</span></td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else</span></td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bismark":</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 ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' &&</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) == "samtools":</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 'This file was produced by samtools stats'</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 ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</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) == "picard":</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 $repeat.input_file</span></td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "samtools_idxstats":</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 "idxstats" 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 $repeat.input_file</span></td> - </tr> - <tr> - <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> - <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' &&</span></td> - </tr> - <tr> - <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> - <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> - <td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "htseq":</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 "__too_low_aQual"</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 $repeat.input_file</span></td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_log":</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 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> - </tr> - <tr> - <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> - <td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' &&</span></td> - </tr> - <tr> - <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> - <td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> - </tr> - <tr> - <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> - <td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_counts":</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 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> - </tr> - <tr> - <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> - <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' &&</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">]]></span></span></<span class="pl-ent">command</span>></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"> <<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span> <span class="pl-e">title</span>=<span class="pl-s"><span class="pl-pds">"</span>Results<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">"</span>1<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Software name<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Which tool was used generate logs?<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span>>FastQC</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span>>Cutadapt/Trim Galore!</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span>>Tophat2</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span>>FeatureCounts (Summary file)</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span>>Samtools (Stats, Flagstat)</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span>>Samtools (Idxstats)</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span>>Picard</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span>>Bismark</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span>>Bowtie2</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span>>HTSeq-Count</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span>>RNA STAR (log)</<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span>>RNA STAR (reads per gene)</<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt, tabular<span class="pl-pds">"</span></span> <span class="pl-e">multiple</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Result file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Select input datasets<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>boolean<span class="pl-pds">"</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">checked</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Save log file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Save the multiQC log file to the history. This is mostly useful for debugging purposes.<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">outputs</span>></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"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>html<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_report.html<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Webpage<span class="pl-pds">"</span></span> /></td> - </tr> - <tr> - <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> - <td id="LC113" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_data/multiqc.log<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Log<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">filter</span>>saveLog</<span class="pl-ent">filter</span>></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"> </<span class="pl-ent">data</span>></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"> </<span class="pl-ent">outputs</span>></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"> <<span class="pl-ent">tests</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>log_fastqc.txt<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc_2.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_cutadapt.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_tophat.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2SE1.txt,bowtie2SE2.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bowtie2SE.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_featurecounts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_picard.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>10000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_htseq.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_log.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_counts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bismark.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools_idxstats.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_all.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>5000<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">test</span>></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"> </<span class="pl-ent">tests</span>></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"> <<span class="pl-ent">help</span>><span class="pl-s"><span class="pl-pds"><![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'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 ("no feature" file; although the "Assigned" 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 &lt;http://engineson.fr/&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">]]></span></span></<span class="pl-ent">help</span>></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"> <<span class="pl-ent">citations</span>></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"> <<span class="pl-ent">citation</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>doi<span class="pl-pds">"</span></span>>10.1093/bioinformatics/btw354</<span class="pl-ent">citation</span>></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"> </<span class="pl-ent">citations</span>></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"></<span class="pl-ent">tool</span>></td> - </tr> -</table> +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"/> + </repeat> + <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Save log file" help="Save the multiQC log file to the history. This is mostly useful for debugging purposes."/> + </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</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> - </div> - - </div> - - <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button> - <div id="jump-to-line" style="display:none"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> - <button type="submit" class="btn">Go</button> -</form> </div> - - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> + <help><![CDATA[ +**What it does** - </div> - </div> - - </div> +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. - -<div class="container site-footer-container"> - <div class="site-footer " role="contentinfo"> - <ul class="site-footer-links float-right"> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact GitHub</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> +**Inputs** - </ul> +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: - <a href="https://github.com" aria-label="Homepage" class="site-footer-mark" title="GitHub"> - <svg aria-hidden="true" class="octicon octicon-mark-github" height="24" version="1.1" viewBox="0 0 16 16" width="24"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> -</a> - <ul class="site-footer-links"> - <li>© 2017 <span title="0.12879s from github-fe143-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li> - </ul> - </div> -</div> - - - - <div id="ajax-error-message" class="ajax-error-message flash flash-error"> - <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg> - <button type="button" class="flash-close js-flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> - <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg> - </button> - You can't perform that action at this time. - </div> - +- Fastqc +- Cutadapt / Trim Galore! +- Tophat2 +- FeatureCounts (summary file with the column header in the first line or as metadata) +- 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) - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/compat-91f98c37fc84eac24836eec2567e9912742094369a04c4eba6e3cd1fa18902d9.js"></script> - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-e2126a97ee9b5ba4bdafd0d42f4910dcb28b9f1df0ba961f8da5850dfbe403db.js"></script> - - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-4ecb65444c34a31ac3796073302ef7c60943d4ca8ebc37ad8502df45e12fbd91.js"></script> - - - - - <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none"> - <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg> - <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <div class="facebox" id="facebox" style="display:none;"> - <div class="facebox-popup"> - <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description"> - </div> - <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal"> - <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg> - </button> - </div> -</div> +---- + +**Integrated by** + +Cyril Monjeaud and Yvan Le Bras +`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility - </body> -</html> - + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btw354</citation> + </citations> +</tool>