Mercurial > repos > engineson > multiqc

comparison multiqc.xml @ 15:d6579f50e622 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author engineson
date Mon, 24 Jul 2017 08:42:27 -0400
parents e17597fc06fb
children
comparison
equal deleted inserted replaced
14:784165ccd3c1 15:d6579f50e622
1 1 <tool id="multiqc" name="multiqc" version="@WRAPPER_VERSION@.0">
2 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 3 <macros>
4 4 <token name="@WRAPPER_VERSION@">1.0.0</token>
5 5 </macros>
6 6 <requirements>
7 <!DOCTYPE html> 7 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>
8 <html lang="en"> 8 </requirements>
9 <head> 9 <version_command>@WRAPPER_VERSION@</version_command>
10 <meta charset="utf-8"> 10 <command detect_errors="aggressive">
11 <link rel="dns-prefetch" href="https://assets-cdn.github.com"> 11 <![CDATA[
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> 12 mkdir multiqc_WDir &&
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> 13
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> 14 #for $i, $repeat in enumerate( $results )
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> 15 mkdir multiqc_WDir/${repeat.software}_${i} &&
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> 16
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> 17 #if str($repeat.software) == "fastqc":
18 18 ## Searches for files named "fastqc_data.txt"
19 19 #for $k, $file in enumerate($repeat.input_file):
20 20 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} &&
21 <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-e04a23d39bf81b7db3c635177756ef51bc171feb440be9e174933c6eb56382da.css" media="all" rel="stylesheet" /> 21 ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &&
22 <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-caabe7e9677dbaa4c88db92fcc52ed61b0def1a9d2e3d3ab196c0a5c81d20d04.css" media="all" rel="stylesheet" /> 22 #end for
23 23 #else if str($repeat.software) == "tophat":
24 24 ## Searches for files ending in "align_summary.txt"
25 <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/site-4ff621027ab732d24efccdbfda10b40d3be645de22ff72aeccd01041076ef761.css" media="all" rel="stylesheet" /> 25 #for $file in $repeat.input_file:
26 26 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' &&
27 27 #end for
28 <meta name="viewport" content="width=device-width"> 28 #else if str($repeat.software) == "bowtie2":
29 29 ## Searches for files containing 'reads; of these;'
30 <title>galaxy_tools/multiqc.xml at master · EnginesOn/galaxy_tools · GitHub</title> 30 #for $file in $repeat.input_file:
31 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> 31 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
32 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> 32 #end for
33 <meta property="fb:app_id" content="1401488693436528"> 33 #else if str($repeat.software) == "cutadapt":
34 34 ## Searches for files containing 'This is cutadapt'
35 35 #for $file in $repeat.input_file:
36 <meta content="https://avatars1.githubusercontent.com/u/18550486?v=3&amp;s=400" property="og:image" /><meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="EnginesOn/galaxy_tools" property="og:title" /><meta content="https://github.com/EnginesOn/galaxy_tools" property="og:url" /><meta content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization" property="og:description" /> 36 cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
37 37 ## replace header for old cutadapt release
38 <link rel="assets" href="https://assets-cdn.github.com/"> 38 sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
39 39 #end for
40 <meta name="pjax-timeout" content="1000"> 40 #else if str($repeat.software) == "featurecounts":
41 41 ## Checks for files ending in '.summary'
42 <meta name="request-id" content="D2E2:424D:D41B1A:1602B95:595F7737" data-pjax-transient> 42 #for $file in $repeat.input_file
43 43 #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1
44 44 echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
45 <meta name="selected-link" value="repo_source" data-pjax-transient> 45 cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
46 46 #else
47 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> 47 ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
48 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> 48 #end if
49 <meta name="google-analytics" content="UA-3769691-2"> 49 #end for
50 50 #else if str($repeat.software) == "bismark":
51 <meta content="collector.githubapp.com" name="octolytics-host" /><meta content="github" name="octolytics-app-id" /><meta content="https://collector.githubapp.com/github-external/browser_event" name="octolytics-event-url" /><meta content="D2E2:424D:D41B1A:1602B95:595F7737" name="octolytics-dimension-request_id" /><meta content="iad" name="octolytics-dimension-region_edge" /><meta content="iad" name="octolytics-dimension-region_render" /> 51 ## Checks for files ending in _SE_report.txt
52 <meta content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" name="analytics-location" /> 52 #for $file in $repeat.input_file
53 53 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' &&
54 54 #end for
55 55 #else if str($repeat.software) == "samtools":
56 56 ## Checks for files containing 'This file was produced by samtools stats'
57 <meta class="js-ga-set" name="dimension1" content="Logged Out"> 57 #for $file in $repeat.input_file
58 58 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
59 59 #end for
60 60 #else if str($repeat.software) == "picard":
61 61 #for $file in $repeat.input_file
62 <meta name="hostname" content="github.com"> 62 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
63 <meta name="user-login" content=""> 63 #end for
64 64 #else if str($repeat.software) == "samtools_idxstats":
65 <meta name="expected-hostname" content="github.com"> 65 ## Checks for files containing "idxstats" in the name
66 <meta name="js-proxy-site-detection-payload" content="NzMyOWRkNmIzYzllZTM1YmZhZDQwY2NlZTI4OGUwYjQ5NjdlMGVkODE4MGE0Y2E1OTQ4MDQwNmU2NDM0NDljOHx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJEMkUyOjQyNEQ6RDQxQjFBOjE2MDJCOTU6NTk1Rjc3MzciLCJ0aW1lc3RhbXAiOjE0OTk0Mjg2NjMsImhvc3QiOiJnaXRodWIuY29tIn0="> 66 #for $file in $repeat.input_file
67 67 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' &&
68 68 #end for
69 <meta name="html-safe-nonce" content="87e506188465adeadea5d03169402db4751ced63"> 69 #else if str($repeat.software) == "htseq":
70 70 ## Checks for files containing "__too_low_aQual"
71 <meta http-equiv="x-pjax-version" content="f47291fda1809c6a5b3a2f5f4848063e"> 71 #for $file in $repeat.input_file
72 72 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
73 73 #end for
74 <link href="https://github.com/EnginesOn/galaxy_tools/commits/master.atom" rel="alternate" title="Recent Commits to galaxy_tools:master" type="application/atom+xml"> 74 #else if str($repeat.software) == "rnastar_log":
75 75 ## Checks for files named Log.final.out
76 <meta name="description" content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization"> 76 #for $k, $file in enumerate($repeat.input_file):
77 <meta name="go-import" content="github.com/EnginesOn/galaxy_tools git https://github.com/EnginesOn/galaxy_tools.git"> 77 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
78 78 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' &&
79 <meta content="18550486" name="octolytics-dimension-user_id" /><meta content="EnginesOn" name="octolytics-dimension-user_login" /><meta content="59100145" name="octolytics-dimension-repository_id" /><meta content="EnginesOn/galaxy_tools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="59100145" name="octolytics-dimension-repository_network_root_id" /><meta content="EnginesOn/galaxy_tools" name="octolytics-dimension-repository_network_root_nwo" /><meta content="false" name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" /> 79 #end for
80 80 #else if str($repeat.software) == "rnastar_counts":
81 81 ## Checks for files named ReadsPerGene.out.tab
82 <link rel="canonical" href="https://github.com/EnginesOn/galaxy_tools/blob/master/tools/multiqc/multiqc.xml" data-pjax-transient> 82 #for $k, $file in enumerate($repeat.input_file):
83 83 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
84 84 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' &&
85 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> 85 #end for
86 86 #end if
87 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> 87 #end for
88 88
89 <link rel="mask-icon" href="https://assets-cdn.github.com/pinned-octocat.svg" color="#000000"> 89 multiqc multiqc_WDir
90 <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> 90 ]]></command>
91 91 <inputs>
92 <meta name="theme-color" content="#1e2327"> 92 <repeat name="results" title="Results" min="1">
93 93 <param name="software" type="select" label="Software name" help="Which tool was used generate logs?">
94 94 <option value="fastqc">FastQC</option>
95 95 <option value="cutadapt">Cutadapt/Trim Galore!</option>
96 </head> 96 <option value="tophat">Tophat2</option>
97 97 <option value="featurecounts">FeatureCounts (Summary file)</option>
98 <body class="logged-out env-production page-blob"> 98 <option value="samtools">Samtools (Stats, Flagstat)</option>
99 99 <option value="samtools_idxstats">Samtools (Idxstats)</option>
100 100 <option value="picard">Picard</option>
101 101 <option value="bismark">Bismark</option>
102 102 <option value="bowtie2">Bowtie2</option>
103 <div class="position-relative js-header-wrapper "> 103 <option value="htseq">HTSeq-Count</option>
104 <a href="#start-of-content" tabindex="1" class="px-2 py-4 show-on-focus js-skip-to-content">Skip to content</a> 104 <option value="rnastar_log">RNA STAR (log)</option>
105 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> 105 <option value="rnastar_counts">RNA STAR (reads per gene)</option>
106 106 </param>
107 107 <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/>
108 108 </repeat>
109 109 <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."/>
110 110 </inputs>
111 111 <outputs>
112 112 <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
113 <header class="site-header js-details-container Details" role="banner"> 113 <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
114 <div class="site-nav-container"> 114 <filter>saveLog</filter>
115 <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> 115 </data>
116 <svg aria-hidden="true" class="octicon octicon-mark-github" height="32" version="1.1" viewBox="0 0 16 16" width="32"><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> 116 </outputs>
117 </a> 117 <tests>
118 118 <test>
119 <button class="btn-link float-right site-header-toggle js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> 119 <repeat name="results">
120 <svg aria-hidden="true" class="octicon octicon-three-bars" height="24" version="1.1" viewBox="0 0 12 16" width="18"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg> 120 <param name="software" value="fastqc" />
121 </button> 121 <param name="input_file" value="fastqc_data.txt" />
122 122 </repeat>
123 <div class="site-header-menu"> 123 <param name="saveLog" value="True"/>
124 <nav class="site-header-nav"> 124 <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/>
125 <a href="/features" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:features" data-selected-links="/features /features/code-review /features/project-management /features/integrations /features"> 125 <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/>
126 Features 126 </test>
127 </a> <a href="/business" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:business" data-selected-links="/business /business/security /business/customers /business"> 127 <test>
128 Business 128 <repeat name="results">
129 </a> <a href="/explore" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:explore" data-selected-links="/explore /trending /trending/developers /stars /integrations /integrations/feature/code /integrations/feature/collaborate /integrations/feature/ship showcases showcases_search showcases_landing /explore"> 129 <param name="software" value="fastqc" />
130 Explore 130 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
131 </a> <a href="/marketplace" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:marketplace" data-selected-links=" /marketplace"> 131 </repeat>
132 Marketplace 132 <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/>
133 </a> <a href="/pricing" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:pricing" data-selected-links="/pricing /pricing/developer /pricing/team /pricing/business-hosted /pricing/business-enterprise /pricing"> 133 </test>
134 Pricing 134 <test>
135 </a> </nav> 135 <repeat name="results">
136 136 <param name="software" value="cutadapt" />
137 <div class="site-header-actions"> 137 <param name="input_file" value="cutadapt.txt" />
138 <div class="header-search scoped-search site-scoped-search js-site-search" role="search"> 138 </repeat>
139 <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="/EnginesOn/galaxy_tools/search" class="js-site-search-form" data-scoped-search-url="/EnginesOn/galaxy_tools/search" data-unscoped-search-url="/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="&#x2713;" /></div> 139 <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/>
140 <label class="form-control header-search-wrapper js-chromeless-input-container"> 140 </test>
141 <a href="/EnginesOn/galaxy_tools/blob/master/tools/multiqc/multiqc.xml" class="header-search-scope no-underline">This repository</a> 141 <test>
142 <input type="text" 142 <repeat name="results">
143 class="form-control header-search-input js-site-search-focus js-site-search-field is-clearable" 143 <param name="software" value="tophat" />
144 data-hotkey="s" 144 <param name="input_file" value="tophat_data.txt" />
145 name="q" 145 </repeat>
146 value="" 146 <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/>
147 placeholder="Search" 147 </test>
148 aria-label="Search this repository" 148 <test>
149 data-unscoped-placeholder="Search GitHub" 149 <repeat name="results">
150 data-scoped-placeholder="Search" 150 <param name="software" value="bowtie2" />
151 autocapitalize="off"> 151 <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" />
152 <input type="hidden" class="js-site-search-type-field" name="type" > 152 </repeat>
153 </label> 153 <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/>
154 </form></div> 154 </test>
155 155 <test>
156 156 <repeat name="results">
157 <a class="text-bold site-header-link" href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools%2Fblob%2Fmaster%2Ftools%2Fmultiqc%2Fmultiqc.xml" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a> 157 <param name="software" value="featurecounts" />
158 <span class="text-gray">or</span> 158 <param name="input_file" value="featurecounts_data.txt" />
159 <a class="text-bold site-header-link" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a> 159 </repeat>
160 </div> 160 <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/>
161 </div> 161 </test>
162 </div> 162 <test>
163 </header> 163 <repeat name="results">
164 164 <param name="software" value="picard" />
165 165 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" />
166 </div> 166 </repeat>
167 167 <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/>
168 <div id="start-of-content" class="show-on-focus"></div> 168 </test>
169 169 <test>
170 <div id="js-flash-container"> 170 <repeat name="results">
171 </div> 171 <param name="software" value="htseq" />
172 172 <param name="input_file" value="htseq_data.txt" />
173 173 </repeat>
174 174 <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/>
175 <div role="main"> 175 </test>
176 <div itemscope itemtype="http://schema.org/SoftwareSourceCode"> 176 <test>
177 <div id="js-repo-pjax-container" data-pjax-container> 177 <repeat name="results">
178 178 <param name="software" value="rnastar_log" />
179 179 <param name="input_file" value="rnastar_log.txt" />
180 180 </repeat>
181 181 <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/>
182 182 </test>
183 183 <test>
184 184 <repeat name="results">
185 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav"> 185 <param name="software" value="rnastar_counts" />
186 <div class="container repohead-details-container"> 186 <param name="input_file" value="rnastar_counts.txt" />
187 187 </repeat>
188 <ul class="pagehead-actions"> 188 <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/>
189 <li> 189 </test>
190 <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools" 190 <test>
191 class="btn btn-sm btn-with-count tooltipped tooltipped-n" 191 <repeat name="results">
192 aria-label="You must be signed in to watch a repository" rel="nofollow"> 192 <param name="software" value="bismark" />
193 <svg aria-hidden="true" class="octicon octicon-eye" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg> 193 <param name="input_file" value="bismark_data.txt" />
194 Watch 194 </repeat>
195 </a> 195 <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>
196 <a class="social-count" href="/EnginesOn/galaxy_tools/watchers" 196 </test>
197 aria-label="3 users are watching this repository"> 197 <test>
198 3 198 <repeat name="results">
199 </a> 199 <param name="software" value="samtools" />
200 200 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
201 </li> 201 </repeat>
202 202 <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>
203 <li> 203 </test>
204 <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools" 204 <test>
205 class="btn btn-sm btn-with-count tooltipped tooltipped-n" 205 <repeat name="results">
206 aria-label="You must be signed in to star a repository" rel="nofollow"> 206 <param name="software" value="samtools_idxstats" />
207 <svg aria-hidden="true" class="octicon octicon-star" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74z"/></svg> 207 <param name="input_file" value="samtools_idxstats.txt" />
208 Star 208 </repeat>
209 </a> 209 <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/>
210 210 </test>
211 <a class="social-count js-social-count" href="/EnginesOn/galaxy_tools/stargazers" 211 <test>
212 aria-label="0 users starred this repository"> 212 <repeat name="results">
213 0 213 <param name="software" value="fastqc" />
214 </a> 214 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
215 215 </repeat>
216 </li> 216 <repeat name="results">
217 217 <param name="software" value="cutadapt" />
218 <li> 218 <param name="input_file" value="cutadapt.txt" />
219 <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools" 219 </repeat>
220 class="btn btn-sm btn-with-count tooltipped tooltipped-n" 220 <repeat name="results">
221 aria-label="You must be signed in to fork a repository" rel="nofollow"> 221 <param name="software" value="tophat" />
222 <svg aria-hidden="true" class="octicon octicon-repo-forked" height="16" version="1.1" viewBox="0 0 10 16" width="10"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> 222 <param name="input_file" value="tophat_data.txt" />
223 Fork 223 </repeat>
224 </a> 224 <repeat name="results">
225 225 <param name="software" value="featurecounts" />
226 <a href="/EnginesOn/galaxy_tools/network" class="social-count" 226 <param name="input_file" value="featurecounts_data.txt" />
227 aria-label="6 users forked this repository"> 227 </repeat>
228 6 228 <repeat name="results">
229 </a> 229 <param name="software" value="picard" />
230 </li> 230 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />
231 </ul> 231 </repeat>
232 232 <repeat name="results">
233 <h1 class="public "> 233 <param name="software" value="bismark" />
234 <svg aria-hidden="true" class="octicon octicon-repo" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> 234 <param name="input_file" value="bismark_data.txt" />
235 <span class="author" itemprop="author"><a href="/EnginesOn" class="url fn" rel="author">EnginesOn</a></span><!-- 235 </repeat>
236 --><span class="path-divider">/</span><!-- 236 <repeat name="results">
237 --><strong itemprop="name"><a href="/EnginesOn/galaxy_tools" data-pjax="#js-repo-pjax-container">galaxy_tools</a></strong> 237 <param name="software" value="samtools" />
238 238 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
239 </h1> 239 </repeat>
240 240 <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/>
241 </div> 241 </test>
242 <div class="container"> 242 </tests>
243 243
244 <nav class="reponav js-repo-nav js-sidenav-container-pjax" 244 <help><![CDATA[
245 itemscope 245 **What it does**
246 itemtype="http://schema.org/BreadcrumbList" 246
247 role="navigation" 247 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.
248 data-pjax="#js-repo-pjax-container"> 248
249 249 **Inputs**
250 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> 250
251 <a href="/EnginesOn/galaxy_tools" class="js-selected-navigation-item selected reponav-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /EnginesOn/galaxy_tools" itemprop="url"> 251 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:
252 <svg aria-hidden="true" class="octicon octicon-code" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg> 252
253 <span itemprop="name">Code</span> 253 - Fastqc
254 <meta itemprop="position" content="1"> 254 - Cutadapt / Trim Galore!
255 </a> </span> 255 - Tophat2
256 256 - FeatureCounts (summary file with the column header in the first line or as metadata)
257 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> 257 - Samtools (stats, flagstat, dxstats)
258 <a href="/EnginesOn/galaxy_tools/issues" class="js-selected-navigation-item reponav-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /EnginesOn/galaxy_tools/issues" itemprop="url"> 258 - Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)
259 <svg aria-hidden="true" class="octicon octicon-issue-opened" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg> 259 - Bismark (Alignment report file)
260 <span itemprop="name">Issues</span> 260 - Bowtie2 (Metrics file)
261 <span class="Counter">0</span> 261 - HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)
262 <meta itemprop="position" content="2"> 262 - RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)
263 </a> </span> 263
264 264 ----
265 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> 265
266 <a href="/EnginesOn/galaxy_tools/pulls" class="js-selected-navigation-item reponav-item" data-hotkey="g p" data-selected-links="repo_pulls /EnginesOn/galaxy_tools/pulls" itemprop="url"> 266 **Integrated by**
267 <svg aria-hidden="true" class="octicon octicon-git-pull-request" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> 267
268 <span itemprop="name">Pull requests</span> 268 Cyril Monjeaud and Yvan Le Bras
269 <span class="Counter">1</span> 269
270 <meta itemprop="position" content="3"> 270 `EnginesOn &lt;http://engineson.fr/&gt;`_ and Rennes GenOuest Bio-informatics Core Facility
271 </a> </span> 271
272 272 ]]></help>
273 <a href="/EnginesOn/galaxy_tools/projects" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /EnginesOn/galaxy_tools/projects"> 273 <citations>
274 <svg aria-hidden="true" class="octicon octicon-project" height="16" version="1.1" viewBox="0 0 15 16" width="15"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> 274 <citation type="doi">10.1093/bioinformatics/btw354</citation>
275 Projects 275 </citations>
276 <span class="Counter" >0</span> 276 </tool>
277 </a>
278
279
280 <div class="reponav-dropdown js-menu-container">
281 <button type="button" class="btn-link reponav-item reponav-dropdown js-menu-target " data-no-toggle aria-expanded="false" aria-haspopup="true">
282 Insights
283 <svg aria-hidden="true" class="octicon octicon-triangle-down v-align-middle text-gray" height="11" version="1.1" viewBox="0 0 12 16" width="8"><path fill-rule="evenodd" d="M0 5l6 6 6-6z"/></svg>
284 </button>
285 <div class="dropdown-menu-content js-menu-content">
286 <div class="dropdown-menu dropdown-menu-sw">
287 <a class="dropdown-item" href="/EnginesOn/galaxy_tools/pulse" data-skip-pjax>
288 <svg aria-hidden="true" class="octicon octicon-pulse" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M11.5 8L8.8 5.4 6.6 8.5 5.5 1.6 2.38 8H0v2h3.6l.9-1.8.9 5.4L9 8.5l1.6 1.5H14V8z"/></svg>
289 Pulse
290 </a>
291 <a class="dropdown-item" href="/EnginesOn/galaxy_tools/graphs" data-skip-pjax>
292 <svg aria-hidden="true" class="octicon octicon-graph" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
293 Graphs
294 </a>
295 </div>
296 </div>
297 </div>
298 </nav>
299
300 </div>
301 </div>
302
303 <div class="container new-discussion-timeline experiment-repo-nav">
304 <div class="repository-content">
305
306
307 <a href="/EnginesOn/galaxy_tools/blob/fa43dee9d5e20fff5df3fe6d50741271b02ede43/tools/multiqc/multiqc.xml" class="d-none js-permalink-shortcut" data-hotkey="y">Permalink</a>
308
309 <!-- blob contrib key: blob_contributors:v21:e59e7b02d9cecabd0ea0af41ae620d5d -->
310
311 <div class="file-navigation js-zeroclipboard-container">
312
313 <div class="select-menu branch-select-menu js-menu-container js-select-menu float-left">
314 <button class=" btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
315
316 type="button" aria-label="Switch branches or tags" aria-expanded="false" aria-haspopup="true">
317 <i>Branch:</i>
318 <span class="js-select-button css-truncate-target">master</span>
319 </button>
320
321 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax>
322
323 <div class="select-menu-modal">
324 <div class="select-menu-header">
325 <svg aria-label="Close" class="octicon octicon-x js-menu-close" height="16" role="img" 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>
326 <span class="select-menu-title">Switch branches/tags</span>
327 </div>
328
329 <div class="select-menu-filters">
330 <div class="select-menu-text-filter">
331 <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="form-control js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
332 </div>
333 <div class="select-menu-tabs">
334 <ul>
335 <li class="select-menu-tab">
336 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a>
337 </li>
338 <li class="select-menu-tab">
339 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a>
340 </li>
341 </ul>
342 </div>
343 </div>
344
345 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu">
346
347 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
348
349
350 <a class="select-menu-item js-navigation-item js-navigation-open selected"
351 href="/EnginesOn/galaxy_tools/blob/master/tools/multiqc/multiqc.xml"
352 data-name="master"
353 data-skip-pjax="true"
354 rel="nofollow">
355 <svg aria-hidden="true" class="octicon octicon-check select-menu-item-icon" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5z"/></svg>
356 <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text">
357 master
358 </span>
359 </a>
360 </div>
361
362 <div class="select-menu-no-results">Nothing to show</div>
363 </div>
364
365 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags">
366 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
367
368
369 </div>
370
371 <div class="select-menu-no-results">Nothing to show</div>
372 </div>
373
374 </div>
375 </div>
376 </div>
377
378 <div class="BtnGroup float-right">
379 <a href="/EnginesOn/galaxy_tools/find/master"
380 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
381 data-pjax
382 data-hotkey="t">
383 Find file
384 </a>
385 <button aria-label="Copy file path to clipboard" class="js-zeroclipboard btn btn-sm BtnGroup-item tooltipped tooltipped-s" data-copied-hint="Copied!" type="button">Copy path</button>
386 </div>
387 <div class="breadcrumb js-zeroclipboard-target">
388 <span class="repo-root js-repo-root"><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools"><span>galaxy_tools</span></a></span></span><span class="separator">/</span><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools/tree/master/tools"><span>tools</span></a></span><span class="separator">/</span><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools/tree/master/tools/multiqc"><span>multiqc</span></a></span><span class="separator">/</span><strong class="final-path">multiqc.xml</strong>
389 </div>
390 </div>
391
392
393 <include-fragment class="commit-tease" src="/EnginesOn/galaxy_tools/contributors/master/tools/multiqc/multiqc.xml">
394 <div>
395 Fetching contributors&hellip;
396 </div>
397
398 <div class="commit-tease-contributors">
399 <img alt="" class="loader-loading float-left" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" />
400 <span class="loader-error">Cannot retrieve contributors at this time</span>
401 </div>
402 </include-fragment>
403 <div class="file">
404 <div class="file-header">
405 <div class="file-actions">
406
407 <div class="BtnGroup">
408 <a href="/EnginesOn/galaxy_tools/raw/master/tools/multiqc/multiqc.xml" class="btn btn-sm BtnGroup-item" id="raw-url">Raw</a>
409 <a href="/EnginesOn/galaxy_tools/blame/master/tools/multiqc/multiqc.xml" class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b">Blame</a>
410 <a href="/EnginesOn/galaxy_tools/commits/master/tools/multiqc/multiqc.xml" class="btn btn-sm BtnGroup-item" rel="nofollow">History</a>
411 </div>
412
413
414 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw"
415 aria-label="You must be signed in to make or propose changes">
416 <svg aria-hidden="true" class="octicon octicon-pencil" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
417 </button>
418 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
419 aria-label="You must be signed in to make or propose changes">
420 <svg aria-hidden="true" class="octicon octicon-trashcan" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg>
421 </button>
422 </div>
423
424 <div class="file-info">
425 277 lines (263 sloc)
426 <span class="file-info-divider"></span>
427 13.7 KB
428 </div>
429 </div>
430
431
432
433 <div itemprop="text" class="blob-wrapper data type-xml">
434 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
435 <tr>
436 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
437 <td id="LC1" class="blob-code blob-code-inner js-file-line">&lt;<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@.0<span class="pl-pds">&quot;</span></span>&gt;</td>
438 </tr>
439 <tr>
440 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
441 <td id="LC2" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">description</span>&gt;aggregate results from bioinformatics analyses into a single report&lt;/<span class="pl-ent">description</span>&gt;</td>
442 </tr>
443 <tr>
444 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
445 <td id="LC3" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">macros</span>&gt;</td>
446 </tr>
447 <tr>
448 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
449 <td id="LC4" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">token</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@<span class="pl-pds">&quot;</span></span>&gt;1.0.0&lt;/<span class="pl-ent">token</span>&gt;</td>
450 </tr>
451 <tr>
452 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
453 <td id="LC5" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">macros</span>&gt;</td>
454 </tr>
455 <tr>
456 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
457 <td id="LC6" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirements</span>&gt;</td>
458 </tr>
459 <tr>
460 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
461 <td id="LC7" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>@WRAPPER_VERSION@<span class="pl-pds">&quot;</span></span>&gt;multiqc&lt;/<span class="pl-ent">requirement</span>&gt;</td>
462 </tr>
463 <tr>
464 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
465 <td id="LC8" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">requirements</span>&gt;</td>
466 </tr>
467 <tr>
468 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
469 <td id="LC9" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">version_command</span>&gt;@WRAPPER_VERSION@&lt;/<span class="pl-ent">version_command</span>&gt;</td>
470 </tr>
471 <tr>
472 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
473 <td id="LC10" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">command</span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>aggressive<span class="pl-pds">&quot;</span></span>&gt;</td>
474 </tr>
475 <tr>
476 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
477 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">&lt;![CDATA[</span></span></td>
478 </tr>
479 <tr>
480 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
481 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s">mkdir multiqc_WDir &amp;&amp;</span></td>
482 </tr>
483 <tr>
484 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
485 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
486 </tr>
487 <tr>
488 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
489 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#for $i, $repeat in enumerate( $results )</span></td>
490 </tr>
491 <tr>
492 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
493 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir multiqc_WDir/${repeat.software}_${i} &amp;&amp;</span></td>
494 </tr>
495 <tr>
496 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
497 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
498 </tr>
499 <tr>
500 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
501 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if str($repeat.software) == &quot;fastqc&quot;:</span></td>
502 </tr>
503 <tr>
504 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
505 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files named &quot;fastqc_data.txt&quot;</span></td>
506 </tr>
507 <tr>
508 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
509 <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>
510 </tr>
511 <tr>
512 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
513 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} &amp;&amp;</span></td>
514 </tr>
515 <tr>
516 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
517 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &amp;&amp;</span></td>
518 </tr>
519 <tr>
520 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
521 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
522 </tr>
523 <tr>
524 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
525 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;tophat&quot;:</span></td>
526 </tr>
527 <tr>
528 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
529 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files ending in &quot;align_summary.txt&quot;</span></td>
530 </tr>
531 <tr>
532 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
533 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
534 </tr>
535 <tr>
536 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
537 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt&#39; &amp;&amp;</span></td>
538 </tr>
539 <tr>
540 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
541 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
542 </tr>
543 <tr>
544 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
545 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;bowtie2&quot;:</span></td>
546 </tr>
547 <tr>
548 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
549 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files containing &#39;reads; of these;&#39;</span></td>
550 </tr>
551 <tr>
552 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
553 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
554 </tr>
555 <tr>
556 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
557 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
558 </tr>
559 <tr>
560 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
561 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
562 </tr>
563 <tr>
564 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
565 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;cutadapt&quot;:</span></td>
566 </tr>
567 <tr>
568 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
569 <td id="LC34" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files containing &#39;This is cutadapt&#39;</span></td>
570 </tr>
571 <tr>
572 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
573 <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
574 </tr>
575 <tr>
576 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
577 <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat &#39;${file}&#39; &gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
578 </tr>
579 <tr>
580 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
581 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## replace header for old cutadapt release</span></td>
582 </tr>
583 <tr>
584 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
585 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> sed -i .old &#39;s/You are running/This is/&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt&#39; &amp;&amp;</span></td>
586 </tr>
587 <tr>
588 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
589 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
590 </tr>
591 <tr>
592 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
593 <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;featurecounts&quot;:</span></td>
594 </tr>
595 <tr>
596 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
597 <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files ending in &#39;.summary&#39;</span></td>
598 </tr>
599 <tr>
600 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
601 <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
602 </tr>
603 <tr>
604 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
605 <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if $file.metadata.column_names and $file.metadata.column_names.find(&#39;,&#39;) != -1</span></td>
606 </tr>
607 <tr>
608 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
609 <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> echo &#39;$file.metadata.column_names.replace(&#39;,&#39;,&#39;\t&#39;).replace(&#39;__ob__u&#39;,&#39;&#39;).replace(&#39;u__sq__&#39;,&#39;&#39;).replace(&#39;__sq__&#39;,&#39;&#39;).replace(&#39;__cb__&#39;,&#39;&#39;)&#39; &gt;&gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
610 </tr>
611 <tr>
612 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
613 <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat &#39;$file&#39; &gt;&gt; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
614 </tr>
615 <tr>
616 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
617 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else</span></td>
618 </tr>
619 <tr>
620 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
621 <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;$file&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary&#39; &amp;&amp;</span></td>
622 </tr>
623 <tr>
624 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
625 <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td>
626 </tr>
627 <tr>
628 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
629 <td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
630 </tr>
631 <tr>
632 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
633 <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;bismark&quot;:</span></td>
634 </tr>
635 <tr>
636 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
637 <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>
638 </tr>
639 <tr>
640 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
641 <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
642 </tr>
643 <tr>
644 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
645 <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s ${file} &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt&#39; &amp;&amp;</span></td>
646 </tr>
647 <tr>
648 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
649 <td id="LC54" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
650 </tr>
651 <tr>
652 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
653 <td id="LC55" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;samtools&quot;:</span></td>
654 </tr>
655 <tr>
656 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
657 <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing &#39;This file was produced by samtools stats&#39;</span></td>
658 </tr>
659 <tr>
660 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
661 <td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
662 </tr>
663 <tr>
664 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
665 <td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s ${file} &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
666 </tr>
667 <tr>
668 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
669 <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
670 </tr>
671 <tr>
672 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
673 <td id="LC60" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;picard&quot;:</span></td>
674 </tr>
675 <tr>
676 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
677 <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
678 </tr>
679 <tr>
680 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
681 <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
682 </tr>
683 <tr>
684 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
685 <td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
686 </tr>
687 <tr>
688 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
689 <td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;samtools_idxstats&quot;:</span></td>
690 </tr>
691 <tr>
692 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
693 <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing &quot;idxstats&quot; in the name</span></td>
694 </tr>
695 <tr>
696 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
697 <td id="LC66" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
698 </tr>
699 <tr>
700 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
701 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt&#39; &amp;&amp;</span></td>
702 </tr>
703 <tr>
704 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
705 <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
706 </tr>
707 <tr>
708 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
709 <td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;htseq&quot;:</span></td>
710 </tr>
711 <tr>
712 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
713 <td id="LC70" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing &quot;__too_low_aQual&quot;</span></td>
714 </tr>
715 <tr>
716 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
717 <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
718 </tr>
719 <tr>
720 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
721 <td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
722 </tr>
723 <tr>
724 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
725 <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
726 </tr>
727 <tr>
728 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
729 <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;rnastar_log&quot;:</span></td>
730 </tr>
731 <tr>
732 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
733 <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>
734 </tr>
735 <tr>
736 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
737 <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>
738 </tr>
739 <tr>
740 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
741 <td id="LC77" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
742 </tr>
743 <tr>
744 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
745 <td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out&#39; &amp;&amp;</span></td>
746 </tr>
747 <tr>
748 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
749 <td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
750 </tr>
751 <tr>
752 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
753 <td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == &quot;rnastar_counts&quot;:</span></td>
754 </tr>
755 <tr>
756 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
757 <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>
758 </tr>
759 <tr>
760 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
761 <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>
762 </tr>
763 <tr>
764 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
765 <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}&#39; &amp;&amp;</span></td>
766 </tr>
767 <tr>
768 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
769 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s &#39;${file}&#39; &#39;multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab&#39; &amp;&amp;</span></td>
770 </tr>
771 <tr>
772 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
773 <td id="LC85" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
774 </tr>
775 <tr>
776 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
777 <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td>
778 </tr>
779 <tr>
780 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
781 <td id="LC87" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#end for</span></td>
782 </tr>
783 <tr>
784 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
785 <td id="LC88" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
786 </tr>
787 <tr>
788 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
789 <td id="LC89" class="blob-code blob-code-inner js-file-line"><span class="pl-s">multiqc multiqc_WDir</span></td>
790 </tr>
791 <tr>
792 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
793 <td id="LC90" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">]]&gt;</span></span>&lt;/<span class="pl-ent">command</span>&gt;</td>
794 </tr>
795 <tr>
796 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
797 <td id="LC91" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">inputs</span>&gt;</td>
798 </tr>
799 <tr>
800 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
801 <td id="LC92" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span> <span class="pl-e">title</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Results<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1<span class="pl-pds">&quot;</span></span>&gt;</td>
802 </tr>
803 <tr>
804 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
805 <td id="LC93" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Software name<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Which tool was used generate logs?<span class="pl-pds">&quot;</span></span>&gt;</td>
806 </tr>
807 <tr>
808 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
809 <td id="LC94" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span>&gt;FastQC&lt;/<span class="pl-ent">option</span>&gt;</td>
810 </tr>
811 <tr>
812 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
813 <td id="LC95" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span>&gt;Cutadapt/Trim Galore!&lt;/<span class="pl-ent">option</span>&gt;</td>
814 </tr>
815 <tr>
816 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
817 <td id="LC96" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span>&gt;Tophat2&lt;/<span class="pl-ent">option</span>&gt;</td>
818 </tr>
819 <tr>
820 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
821 <td id="LC97" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span>&gt;FeatureCounts (Summary file)&lt;/<span class="pl-ent">option</span>&gt;</td>
822 </tr>
823 <tr>
824 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
825 <td id="LC98" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span>&gt;Samtools (Stats, Flagstat)&lt;/<span class="pl-ent">option</span>&gt;</td>
826 </tr>
827 <tr>
828 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
829 <td id="LC99" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats<span class="pl-pds">&quot;</span></span>&gt;Samtools (Idxstats)&lt;/<span class="pl-ent">option</span>&gt;</td>
830 </tr>
831 <tr>
832 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
833 <td id="LC100" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span>&gt;Picard&lt;/<span class="pl-ent">option</span>&gt;</td>
834 </tr>
835 <tr>
836 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
837 <td id="LC101" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span>&gt;Bismark&lt;/<span class="pl-ent">option</span>&gt;</td>
838 </tr>
839 <tr>
840 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
841 <td id="LC102" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2<span class="pl-pds">&quot;</span></span>&gt;Bowtie2&lt;/<span class="pl-ent">option</span>&gt;</td>
842 </tr>
843 <tr>
844 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
845 <td id="LC103" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq<span class="pl-pds">&quot;</span></span>&gt;HTSeq-Count&lt;/<span class="pl-ent">option</span>&gt;</td>
846 </tr>
847 <tr>
848 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
849 <td id="LC104" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log<span class="pl-pds">&quot;</span></span>&gt;RNA STAR (log)&lt;/<span class="pl-ent">option</span>&gt;</td>
850 </tr>
851 <tr>
852 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
853 <td id="LC105" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts<span class="pl-pds">&quot;</span></span>&gt;RNA STAR (reads per gene)&lt;/<span class="pl-ent">option</span>&gt;</td>
854 </tr>
855 <tr>
856 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
857 <td id="LC106" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
858 </tr>
859 <tr>
860 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
861 <td id="LC107" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>txt, tabular<span class="pl-pds">&quot;</span></span> <span class="pl-e">multiple</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Result file<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Select input datasets<span class="pl-pds">&quot;</span></span>/&gt;</td>
862 </tr>
863 <tr>
864 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
865 <td id="LC108" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
866 </tr>
867 <tr>
868 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
869 <td id="LC109" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>saveLog<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>boolean<span class="pl-pds">&quot;</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>false<span class="pl-pds">&quot;</span></span> <span class="pl-e">checked</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>false<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Save log file<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Save the multiQC log file to the history. This is mostly useful for debugging purposes.<span class="pl-pds">&quot;</span></span>/&gt;</td>
870 </tr>
871 <tr>
872 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
873 <td id="LC110" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">inputs</span>&gt;</td>
874 </tr>
875 <tr>
876 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
877 <td id="LC111" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">outputs</span>&gt;</td>
878 </tr>
879 <tr>
880 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
881 <td id="LC112" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html<span class="pl-pds">&quot;</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc_report.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>${tool.name} on ${on_string}: Webpage<span class="pl-pds">&quot;</span></span> /&gt;</td>
882 </tr>
883 <tr>
884 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
885 <td id="LC113" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>txt<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>text_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>multiqc_data/multiqc.log<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>${tool.name} on ${on_string}: Log<span class="pl-pds">&quot;</span></span>&gt;</td>
886 </tr>
887 <tr>
888 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
889 <td id="LC114" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">filter</span>&gt;saveLog&lt;/<span class="pl-ent">filter</span>&gt;</td>
890 </tr>
891 <tr>
892 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
893 <td id="LC115" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">data</span>&gt;</td>
894 </tr>
895 <tr>
896 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
897 <td id="LC116" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">outputs</span>&gt;</td>
898 </tr>
899 <tr>
900 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
901 <td id="LC117" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">tests</span>&gt;</td>
902 </tr>
903 <tr>
904 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
905 <td id="LC118" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
906 </tr>
907 <tr>
908 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
909 <td id="LC119" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
910 </tr>
911 <tr>
912 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
913 <td id="LC120" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
914 </tr>
915 <tr>
916 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
917 <td id="LC121" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
918 </tr>
919 <tr>
920 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
921 <td id="LC122" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
922 </tr>
923 <tr>
924 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
925 <td id="LC123" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>saveLog<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>/&gt;</td>
926 </tr>
927 <tr>
928 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
929 <td id="LC124" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_fastqc.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
930 </tr>
931 <tr>
932 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
933 <td id="LC125" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>text_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>log_fastqc.txt<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
934 </tr>
935 <tr>
936 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
937 <td id="LC126" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
938 </tr>
939 <tr>
940 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
941 <td id="LC127" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
942 </tr>
943 <tr>
944 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
945 <td id="LC128" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
946 </tr>
947 <tr>
948 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
949 <td id="LC129" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
950 </tr>
951 <tr>
952 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
953 <td id="LC130" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
954 </tr>
955 <tr>
956 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
957 <td id="LC131" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
958 </tr>
959 <tr>
960 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
961 <td id="LC132" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_fastqc_2.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
962 </tr>
963 <tr>
964 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
965 <td id="LC133" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
966 </tr>
967 <tr>
968 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
969 <td id="LC134" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
970 </tr>
971 <tr>
972 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
973 <td id="LC135" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
974 </tr>
975 <tr>
976 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
977 <td id="LC136" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span> /&gt;</td>
978 </tr>
979 <tr>
980 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
981 <td id="LC137" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
982 </tr>
983 <tr>
984 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
985 <td id="LC138" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
986 </tr>
987 <tr>
988 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
989 <td id="LC139" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_cutadapt.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
990 </tr>
991 <tr>
992 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
993 <td id="LC140" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
994 </tr>
995 <tr>
996 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
997 <td id="LC141" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
998 </tr>
999 <tr>
1000 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
1001 <td id="LC142" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1002 </tr>
1003 <tr>
1004 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
1005 <td id="LC143" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span> /&gt;</td>
1006 </tr>
1007 <tr>
1008 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
1009 <td id="LC144" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1010 </tr>
1011 <tr>
1012 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
1013 <td id="LC145" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1014 </tr>
1015 <tr>
1016 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
1017 <td id="LC146" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_tophat.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1018 </tr>
1019 <tr>
1020 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
1021 <td id="LC147" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1022 </tr>
1023 <tr>
1024 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
1025 <td id="LC148" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1026 </tr>
1027 <tr>
1028 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
1029 <td id="LC149" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1030 </tr>
1031 <tr>
1032 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
1033 <td id="LC150" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2<span class="pl-pds">&quot;</span></span> /&gt;</td>
1034 </tr>
1035 <tr>
1036 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
1037 <td id="LC151" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2SE1.txt,bowtie2SE2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1038 </tr>
1039 <tr>
1040 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
1041 <td id="LC152" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1042 </tr>
1043 <tr>
1044 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
1045 <td id="LC153" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_bowtie2SE.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1046 </tr>
1047 <tr>
1048 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
1049 <td id="LC154" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1050 </tr>
1051 <tr>
1052 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
1053 <td id="LC155" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1054 </tr>
1055 <tr>
1056 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
1057 <td id="LC156" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1058 </tr>
1059 <tr>
1060 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
1061 <td id="LC157" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span> /&gt;</td>
1062 </tr>
1063 <tr>
1064 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
1065 <td id="LC158" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1066 </tr>
1067 <tr>
1068 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
1069 <td id="LC159" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1070 </tr>
1071 <tr>
1072 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
1073 <td id="LC160" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_featurecounts.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1074 </tr>
1075 <tr>
1076 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
1077 <td id="LC161" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1078 </tr>
1079 <tr>
1080 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
1081 <td id="LC162" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1082 </tr>
1083 <tr>
1084 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
1085 <td id="LC163" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1086 </tr>
1087 <tr>
1088 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
1089 <td id="LC164" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span> /&gt;</td>
1090 </tr>
1091 <tr>
1092 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
1093 <td id="LC165" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1094 </tr>
1095 <tr>
1096 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
1097 <td id="LC166" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1098 </tr>
1099 <tr>
1100 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
1101 <td id="LC167" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_picard.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>10000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1102 </tr>
1103 <tr>
1104 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
1105 <td id="LC168" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1106 </tr>
1107 <tr>
1108 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
1109 <td id="LC169" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1110 </tr>
1111 <tr>
1112 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
1113 <td id="LC170" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1114 </tr>
1115 <tr>
1116 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
1117 <td id="LC171" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq<span class="pl-pds">&quot;</span></span> /&gt;</td>
1118 </tr>
1119 <tr>
1120 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
1121 <td id="LC172" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>htseq_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1122 </tr>
1123 <tr>
1124 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
1125 <td id="LC173" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1126 </tr>
1127 <tr>
1128 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
1129 <td id="LC174" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_htseq.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1130 </tr>
1131 <tr>
1132 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
1133 <td id="LC175" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1134 </tr>
1135 <tr>
1136 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
1137 <td id="LC176" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1138 </tr>
1139 <tr>
1140 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
1141 <td id="LC177" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1142 </tr>
1143 <tr>
1144 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
1145 <td id="LC178" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log<span class="pl-pds">&quot;</span></span> /&gt;</td>
1146 </tr>
1147 <tr>
1148 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
1149 <td id="LC179" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_log.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1150 </tr>
1151 <tr>
1152 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
1153 <td id="LC180" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1154 </tr>
1155 <tr>
1156 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
1157 <td id="LC181" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_rnastar_log.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1158 </tr>
1159 <tr>
1160 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
1161 <td id="LC182" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1162 </tr>
1163 <tr>
1164 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
1165 <td id="LC183" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1166 </tr>
1167 <tr>
1168 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
1169 <td id="LC184" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1170 </tr>
1171 <tr>
1172 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
1173 <td id="LC185" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts<span class="pl-pds">&quot;</span></span> /&gt;</td>
1174 </tr>
1175 <tr>
1176 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
1177 <td id="LC186" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>rnastar_counts.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1178 </tr>
1179 <tr>
1180 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
1181 <td id="LC187" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1182 </tr>
1183 <tr>
1184 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
1185 <td id="LC188" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_rnastar_counts.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1186 </tr>
1187 <tr>
1188 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
1189 <td id="LC189" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1190 </tr>
1191 <tr>
1192 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
1193 <td id="LC190" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1194 </tr>
1195 <tr>
1196 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
1197 <td id="LC191" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1198 </tr>
1199 <tr>
1200 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
1201 <td id="LC192" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span> /&gt;</td>
1202 </tr>
1203 <tr>
1204 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
1205 <td id="LC193" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1206 </tr>
1207 <tr>
1208 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
1209 <td id="LC194" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1210 </tr>
1211 <tr>
1212 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
1213 <td id="LC195" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_bismark.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1214 </tr>
1215 <tr>
1216 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
1217 <td id="LC196" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1218 </tr>
1219 <tr>
1220 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
1221 <td id="LC197" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1222 </tr>
1223 <tr>
1224 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
1225 <td id="LC198" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1226 </tr>
1227 <tr>
1228 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
1229 <td id="LC199" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span> /&gt;</td>
1230 </tr>
1231 <tr>
1232 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
1233 <td id="LC200" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1234 </tr>
1235 <tr>
1236 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
1237 <td id="LC201" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1238 </tr>
1239 <tr>
1240 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
1241 <td id="LC202" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_samtools.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1242 </tr>
1243 <tr>
1244 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
1245 <td id="LC203" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1246 </tr>
1247 <tr>
1248 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
1249 <td id="LC204" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1250 </tr>
1251 <tr>
1252 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
1253 <td id="LC205" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1254 </tr>
1255 <tr>
1256 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
1257 <td id="LC206" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats<span class="pl-pds">&quot;</span></span> /&gt;</td>
1258 </tr>
1259 <tr>
1260 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
1261 <td id="LC207" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_idxstats.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1262 </tr>
1263 <tr>
1264 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
1265 <td id="LC208" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1266 </tr>
1267 <tr>
1268 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
1269 <td id="LC209" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_samtools_idxstats.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1270 </tr>
1271 <tr>
1272 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
1273 <td id="LC210" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1274 </tr>
1275 <tr>
1276 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
1277 <td id="LC211" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1278 </tr>
1279 <tr>
1280 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
1281 <td id="LC212" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1282 </tr>
1283 <tr>
1284 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
1285 <td id="LC213" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc<span class="pl-pds">&quot;</span></span> /&gt;</td>
1286 </tr>
1287 <tr>
1288 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
1289 <td id="LC214" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1290 </tr>
1291 <tr>
1292 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
1293 <td id="LC215" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1294 </tr>
1295 <tr>
1296 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
1297 <td id="LC216" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1298 </tr>
1299 <tr>
1300 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
1301 <td id="LC217" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1302 </tr>
1303 <tr>
1304 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
1305 <td id="LC218" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cutadapt.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1306 </tr>
1307 <tr>
1308 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
1309 <td id="LC219" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1310 </tr>
1311 <tr>
1312 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
1313 <td id="LC220" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1314 </tr>
1315 <tr>
1316 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
1317 <td id="LC221" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat<span class="pl-pds">&quot;</span></span> /&gt;</td>
1318 </tr>
1319 <tr>
1320 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
1321 <td id="LC222" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>tophat_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1322 </tr>
1323 <tr>
1324 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
1325 <td id="LC223" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1326 </tr>
1327 <tr>
1328 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
1329 <td id="LC224" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1330 </tr>
1331 <tr>
1332 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
1333 <td id="LC225" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts<span class="pl-pds">&quot;</span></span> /&gt;</td>
1334 </tr>
1335 <tr>
1336 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
1337 <td id="LC226" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>featurecounts_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1338 </tr>
1339 <tr>
1340 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
1341 <td id="LC227" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1342 </tr>
1343 <tr>
1344 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
1345 <td id="LC228" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1346 </tr>
1347 <tr>
1348 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
1349 <td id="LC229" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>picard<span class="pl-pds">&quot;</span></span> /&gt;</td>
1350 </tr>
1351 <tr>
1352 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
1353 <td id="LC230" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1354 </tr>
1355 <tr>
1356 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
1357 <td id="LC231" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1358 </tr>
1359 <tr>
1360 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
1361 <td id="LC232" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1362 </tr>
1363 <tr>
1364 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
1365 <td id="LC233" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark<span class="pl-pds">&quot;</span></span> /&gt;</td>
1366 </tr>
1367 <tr>
1368 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
1369 <td id="LC234" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>bismark_data.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1370 </tr>
1371 <tr>
1372 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
1373 <td id="LC235" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1374 </tr>
1375 <tr>
1376 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
1377 <td id="LC236" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>&gt;</td>
1378 </tr>
1379 <tr>
1380 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
1381 <td id="LC237" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>software<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools<span class="pl-pds">&quot;</span></span> /&gt;</td>
1382 </tr>
1383 <tr>
1384 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
1385 <td id="LC238" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>input_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">&quot;</span></span> /&gt;</td>
1386 </tr>
1387 <tr>
1388 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
1389 <td id="LC239" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">repeat</span>&gt;</td>
1390 </tr>
1391 <tr>
1392 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
1393 <td id="LC240" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>report_all.html<span class="pl-pds">&quot;</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sim_size<span class="pl-pds">&quot;</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>5000<span class="pl-pds">&quot;</span></span>/&gt;</td>
1394 </tr>
1395 <tr>
1396 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
1397 <td id="LC241" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1398 </tr>
1399 <tr>
1400 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
1401 <td id="LC242" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">tests</span>&gt;</td>
1402 </tr>
1403 <tr>
1404 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
1405 <td id="LC243" class="blob-code blob-code-inner js-file-line">
1406 </td>
1407 </tr>
1408 <tr>
1409 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
1410 <td id="LC244" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">help</span>&gt;<span class="pl-s"><span class="pl-pds">&lt;![CDATA[</span></span></td>
1411 </tr>
1412 <tr>
1413 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
1414 <td id="LC245" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**What it does**</span></td>
1415 </tr>
1416 <tr>
1417 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
1418 <td id="LC246" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1419 </tr>
1420 <tr>
1421 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
1422 <td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-s">MultiQC aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It&#39;s a general use tool, perfect for summarizing the output from numerous bioinformatics tools.</span></td>
1423 </tr>
1424 <tr>
1425 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
1426 <td id="LC248" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1427 </tr>
1428 <tr>
1429 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
1430 <td id="LC249" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Inputs**</span></td>
1431 </tr>
1432 <tr>
1433 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
1434 <td id="LC250" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1435 </tr>
1436 <tr>
1437 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
1438 <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>
1439 </tr>
1440 <tr>
1441 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
1442 <td id="LC252" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1443 </tr>
1444 <tr>
1445 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
1446 <td id="LC253" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Fastqc</span></td>
1447 </tr>
1448 <tr>
1449 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
1450 <td id="LC254" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Cutadapt / Trim Galore!</span></td>
1451 </tr>
1452 <tr>
1453 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
1454 <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Tophat2</span></td>
1455 </tr>
1456 <tr>
1457 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
1458 <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>
1459 </tr>
1460 <tr>
1461 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
1462 <td id="LC257" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Samtools (stats, flagstat, dxstats)</span></td>
1463 </tr>
1464 <tr>
1465 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
1466 <td id="LC258" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)</span></td>
1467 </tr>
1468 <tr>
1469 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
1470 <td id="LC259" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bismark (Alignment report file)</span></td>
1471 </tr>
1472 <tr>
1473 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
1474 <td id="LC260" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bowtie2 (Metrics file)</span></td>
1475 </tr>
1476 <tr>
1477 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
1478 <td id="LC261" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- HTSeq-count (&quot;no feature&quot; file; although the &quot;Assigned&quot; metric is always 0)</span></td>
1479 </tr>
1480 <tr>
1481 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
1482 <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>
1483 </tr>
1484 <tr>
1485 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
1486 <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1487 </tr>
1488 <tr>
1489 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
1490 <td id="LC264" class="blob-code blob-code-inner js-file-line"><span class="pl-s">----</span></td>
1491 </tr>
1492 <tr>
1493 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
1494 <td id="LC265" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1495 </tr>
1496 <tr>
1497 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
1498 <td id="LC266" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Integrated by**</span></td>
1499 </tr>
1500 <tr>
1501 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
1502 <td id="LC267" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1503 </tr>
1504 <tr>
1505 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
1506 <td id="LC268" class="blob-code blob-code-inner js-file-line"><span class="pl-s">Cyril Monjeaud and Yvan Le Bras</span></td>
1507 </tr>
1508 <tr>
1509 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
1510 <td id="LC269" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1511 </tr>
1512 <tr>
1513 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
1514 <td id="LC270" class="blob-code blob-code-inner js-file-line"><span class="pl-s">`EnginesOn &amp;lt;http://engineson.fr/&amp;gt;`_ and Rennes GenOuest Bio-informatics Core Facility</span></td>
1515 </tr>
1516 <tr>
1517 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
1518 <td id="LC271" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
1519 </tr>
1520 <tr>
1521 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
1522 <td id="LC272" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">]]&gt;</span></span>&lt;/<span class="pl-ent">help</span>&gt;</td>
1523 </tr>
1524 <tr>
1525 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
1526 <td id="LC273" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">citations</span>&gt;</td>
1527 </tr>
1528 <tr>
1529 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
1530 <td id="LC274" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">citation</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>doi<span class="pl-pds">&quot;</span></span>&gt;10.1093/bioinformatics/btw354&lt;/<span class="pl-ent">citation</span>&gt;</td>
1531 </tr>
1532 <tr>
1533 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
1534 <td id="LC275" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">citations</span>&gt;</td>
1535 </tr>
1536 <tr>
1537 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
1538 <td id="LC276" class="blob-code blob-code-inner js-file-line">&lt;/<span class="pl-ent">tool</span>&gt;</td>
1539 </tr>
1540 </table>
1541
1542 </div>
1543
1544 </div>
1545
1546 <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button>
1547 <div id="jump-to-line" style="display:none">
1548 <!-- '"` --><!-- </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="&#x2713;" /></div>
1549 <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" aria-label="Jump to line" autofocus>
1550 <button type="submit" class="btn">Go</button>
1551 </form> </div>
1552
1553 </div>
1554 <div class="modal-backdrop js-touch-events"></div>
1555 </div>
1556
1557 </div>
1558 </div>
1559
1560 </div>
1561
1562
1563 <div class="container site-footer-container">
1564 <div class="site-footer " role="contentinfo">
1565 <ul class="site-footer-links float-right">
1566 <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact GitHub</a></li>
1567 <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
1568 <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
1569 <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
1570 <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
1571 <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
1572
1573 </ul>
1574
1575 <a href="https://github.com" aria-label="Homepage" class="site-footer-mark" title="GitHub">
1576 <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>
1577 </a>
1578 <ul class="site-footer-links">
1579 <li>&copy; 2017 <span title="0.12879s from github-fe143-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
1580 <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
1581 <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
1582 <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
1583 <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
1584 <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li>
1585 </ul>
1586 </div>
1587 </div>
1588
1589
1590
1591 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
1592 <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>
1593 <button type="button" class="flash-close js-flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
1594 <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>
1595 </button>
1596 You can't perform that action at this time.
1597 </div>
1598
1599
1600 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/compat-91f98c37fc84eac24836eec2567e9912742094369a04c4eba6e3cd1fa18902d9.js"></script>
1601 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-e2126a97ee9b5ba4bdafd0d42f4910dcb28b9f1df0ba961f8da5850dfbe403db.js"></script>
1602
1603 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-4ecb65444c34a31ac3796073302ef7c60943d4ca8ebc37ad8502df45e12fbd91.js"></script>
1604
1605
1606
1607
1608 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none">
1609 <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>
1610 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
1611 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
1612 </div>
1613 <div class="facebox" id="facebox" style="display:none;">
1614 <div class="facebox-popup">
1615 <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description">
1616 </div>
1617 <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal">
1618 <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>
1619 </button>
1620 </div>
1621 </div>
1622
1623
1624 </body>
1625 </html>
1626