Mercurial > repos > engineson > multiqc
comparison multiqc.xml @ 13:e17597fc06fb draft
Updated xml file from github
author | engineson |
---|---|
date | Fri, 07 Jul 2017 07:57:43 -0400 |
parents | c503e1c1fbad |
children | d6579f50e622 |
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12:e95b3d2c3dc0 | 13:e17597fc06fb |
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1 <tool id="multiqc" name="multiqc" version="1.0.0.0"> | 1 |
2 <description>aggregate results from bioinformatics analyses into a single report</description> | 2 |
3 <requirements> | 3 |
4 <requirement type="package" version="1.0.0">multiqc</requirement> | 4 |
5 </requirements> | 5 |
6 <stdio> | 6 |
7 <exit_code range="1:" /> | 7 <!DOCTYPE html> |
8 </stdio> | 8 <html lang="en"> |
9 <command> | 9 <head> |
10 mkdir multiqc_WDir; | 10 <meta charset="utf-8"> |
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26 | |
27 | |
28 <meta name="viewport" content="width=device-width"> | |
29 | |
30 <title>galaxy_tools/multiqc.xml at master · EnginesOn/galaxy_tools · GitHub</title> | |
31 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> | |
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76 <meta name="description" content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization"> | |
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82 <link rel="canonical" href="https://github.com/EnginesOn/galaxy_tools/blob/master/tools/multiqc/multiqc.xml" data-pjax-transient> | |
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85 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> | |
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92 <meta name="theme-color" content="#1e2327"> | |
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96 </head> | |
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98 <body class="logged-out env-production page-blob"> | |
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103 <div class="position-relative js-header-wrapper "> | |
104 <a href="#start-of-content" tabindex="1" class="px-2 py-4 show-on-focus js-skip-to-content">Skip to content</a> | |
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132 Marketplace | |
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134 Pricing | |
135 </a> </nav> | |
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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="✓" /></div> | |
140 <label class="form-control header-search-wrapper js-chromeless-input-container"> | |
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142 <input type="text" | |
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153 </label> | |
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158 <span class="text-gray">or</span> | |
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208 Star | |
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212 aria-label="0 users starred this repository"> | |
213 0 | |
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223 Fork | |
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227 aria-label="6 users forked this repository"> | |
228 6 | |
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242 <div class="container"> | |
11 | 243 |
12 #for $i, $repeat in enumerate( $results ) | 244 <nav class="reponav js-repo-nav js-sidenav-container-pjax" |
13 mkdir multiqc_WDir/${repeat.software}_${i}; | 245 itemscope |
14 | 246 itemtype="http://schema.org/BreadcrumbList" |
15 #if str($repeat.software) == "fastqc": | 247 role="navigation" |
16 ## Searches for files named "fastqc_data.txt" | 248 data-pjax="#js-repo-pjax-container"> |
17 #for $k, $file in enumerate($repeat.input_file): | 249 |
18 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k}; | 250 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> |
19 ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt; | 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"> |
20 #end for | 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> |
21 #else if str($repeat.software) == "tophat": | 253 <span itemprop="name">Code</span> |
22 ## Searches for files ending in "align_summary.txt" | 254 <meta itemprop="position" content="1"> |
23 #for $file in $repeat.input_file: | 255 </a> </span> |
24 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}align_summary.txt'; | 256 |
25 #end for | 257 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> |
26 #else if str($repeat.software) == "bowtie2": | 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"> |
27 ## Searches for files containing 'reads; of these;' | 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> |
28 #for $file in $repeat.input_file: | 260 <span itemprop="name">Issues</span> |
29 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | 261 <span class="Counter">0</span> |
30 #end for | 262 <meta itemprop="position" content="2"> |
31 #else if str($repeat.software) == "cutadapt": | 263 </a> </span> |
32 ## Searches for files containing 'This is cutadapt' | 264 |
33 #for $file in $repeat.input_file: | 265 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> |
34 cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | 266 <a href="/EnginesOn/galaxy_tools/pulls" class="js-selected-navigation-item reponav-item" data-hotkey="g p" data-selected-links="repo_pulls /EnginesOn/galaxy_tools/pulls" itemprop="url"> |
35 ## replace header for old cutadapt release | 267 <svg aria-hidden="true" class="octicon octicon-git-pull-request" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> |
36 sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | 268 <span itemprop="name">Pull requests</span> |
37 #end for | 269 <span class="Counter">1</span> |
38 #else if str($repeat.software) == "featurecounts": | 270 <meta itemprop="position" content="3"> |
39 ## Checks for files ending in '.summary' | 271 </a> </span> |
40 #for $k, $file in enumerate($repeat.input_file): | 272 |
41 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k}; | 273 <a href="/EnginesOn/galaxy_tools/projects" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /EnginesOn/galaxy_tools/projects"> |
42 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/file_${k}/${file.display_name}.summary'; | 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> |
43 #end for | 275 Projects |
44 #else if str($repeat.software) == "bismark": | 276 <span class="Counter" >0</span> |
45 ## Checks for files ending in _SE_report.txt | 277 </a> |
46 #for $file in $repeat.input_file | 278 |
47 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_SE_report.txt'; | 279 |
48 #end for | 280 <div class="reponav-dropdown js-menu-container"> |
49 #else if str($repeat.software) == "samtools": | 281 <button type="button" class="btn-link reponav-item reponav-dropdown js-menu-target " data-no-toggle aria-expanded="false" aria-haspopup="true"> |
50 ## Checks for files containing 'This file was produced by samtools stats' | 282 Insights |
51 #for $file in $repeat.input_file | 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> |
52 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | 284 </button> |
53 #end for | 285 <div class="dropdown-menu-content js-menu-content"> |
54 #else if str($repeat.software) == "picard": | 286 <div class="dropdown-menu dropdown-menu-sw"> |
55 #for $file in $repeat.input_file | 287 <a class="dropdown-item" href="/EnginesOn/galaxy_tools/pulse" data-skip-pjax> |
56 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | 288 <svg aria-hidden="true" class="octicon octicon-pulse" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M11.5 8L8.8 5.4 6.6 8.5 5.5 1.6 2.38 8H0v2h3.6l.9-1.8.9 5.4L9 8.5l1.6 1.5H14V8z"/></svg> |
57 #end for | 289 Pulse |
58 #else if str($repeat.software) == "samtools_idxstats": | 290 </a> |
59 ## Checks for files containing "idxstats" in the name | 291 <a class="dropdown-item" href="/EnginesOn/galaxy_tools/graphs" data-skip-pjax> |
60 #for $file in $repeat.input_file | 292 <svg aria-hidden="true" class="octicon octicon-graph" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg> |
61 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_idxstats.txt'; | 293 Graphs |
62 #end for | 294 </a> |
63 #else if str($repeat.software) == "htseq": | 295 </div> |
64 ## Checks for files containing "__too_low_aQual" | 296 </div> |
65 #for $file in $repeat.input_file | 297 </div> |
66 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | 298 </nav> |
67 #end for | 299 |
68 #else if str($repeat.software) == "rnastar_log": | 300 </div> |
69 ## Checks for files named Log.final.out | 301 </div> |
70 #for $k, $file in enumerate($repeat.input_file): | 302 |
71 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | 303 <div class="container new-discussion-timeline experiment-repo-nav"> |
72 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/Log.final.out'; | 304 <div class="repository-content"> |
73 #end for | 305 |
74 #else if str($repeat.software) == "rnastar_counts": | 306 |
75 ## Checks for files named ReadsPerGene.out.tab | 307 <a href="/EnginesOn/galaxy_tools/blob/fa43dee9d5e20fff5df3fe6d50741271b02ede43/tools/multiqc/multiqc.xml" class="d-none js-permalink-shortcut" data-hotkey="y">Permalink</a> |
76 #for $k, $file in enumerate($repeat.input_file): | 308 |
77 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | 309 <!-- blob contrib key: blob_contributors:v21:e59e7b02d9cecabd0ea0af41ae620d5d --> |
78 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/ReadsPerGene.out.tab'; | 310 |
79 #end for | 311 <div class="file-navigation js-zeroclipboard-container"> |
80 #end if | 312 |
81 #end for | 313 <div class="select-menu branch-select-menu js-menu-container js-select-menu float-left"> |
82 | 314 <button class=" btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w" |
83 multiqc multiqc_WDir; | 315 |
84 | 316 type="button" aria-label="Switch branches or tags" aria-expanded="false" aria-haspopup="true"> |
85 </command> | 317 <i>Branch:</i> |
86 <inputs> | 318 <span class="js-select-button css-truncate-target">master</span> |
87 <repeat name="results" title="Results" min="1"> | 319 </button> |
88 <param name="software" type="select" label="Software name" help="Which tool was used generate logs?"> | 320 |
89 <option value="fastqc">FastQC</option> | 321 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax> |
90 <option value="cutadapt">Cutadapt/Trim Galore!</option> | 322 |
91 <option value="tophat">Tophat2</option> | 323 <div class="select-menu-modal"> |
92 <option value="featurecounts">FeatureCounts (Summary file)</option> | 324 <div class="select-menu-header"> |
93 <option value="samtools">Samtools (Stats, Flagstat)</option> | 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> |
94 <option value="samtools_idxstats">Samtools (Idxstats)</option> | 326 <span class="select-menu-title">Switch branches/tags</span> |
95 <option value="picard">Picard</option> | 327 </div> |
96 <option value="bismark">Bismark</option> | 328 |
97 <option value="bowtie2">Bowtie2</option> | 329 <div class="select-menu-filters"> |
98 <option value="htseq">HTSeq-Count</option> | 330 <div class="select-menu-text-filter"> |
99 <option value="rnastar_log">RNA STAR (log)</option> | 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"> |
100 <option value="rnastar_counts">RNA STAR (reads per gene)</option> | 332 </div> |
101 </param> | 333 <div class="select-menu-tabs"> |
102 <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/> | 334 <ul> |
103 <param name="saveLog" type="boolean" checked="false" label="Save log file" help="Save the multiQC log file to the history. This is mostly useful for debugging purposes."/> | 335 <li class="select-menu-tab"> |
104 </repeat> | 336 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a> |
105 </inputs> | 337 </li> |
106 <outputs> | 338 <li class="select-menu-tab"> |
107 <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" /> | 339 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a> |
108 <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> | 340 </li> |
109 <filter>saveLog is True</filter> | 341 </ul> |
110 </data> | 342 </div> |
111 </outputs> | 343 </div> |
112 <tests> | 344 |
113 <test> | 345 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu"> |
114 <repeat name="results"> | 346 |
115 <param name="software" value="fastqc" /> | 347 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> |
116 <param name="input_file" value="fastqc_data.txt" /> | 348 |
117 </repeat> | 349 |
118 <param name="saveLog" value="True"/> | 350 <a class="select-menu-item js-navigation-item js-navigation-open selected" |
119 <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/> | 351 href="/EnginesOn/galaxy_tools/blob/master/tools/multiqc/multiqc.xml" |
120 <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/> | 352 data-name="master" |
121 </test> | 353 data-skip-pjax="true" |
122 <test> | 354 rel="nofollow"> |
123 <repeat name="results"> | 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> |
124 <param name="software" value="fastqc" /> | 356 <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> |
125 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | 357 master |
126 </repeat> | 358 </span> |
127 <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/> | 359 </a> |
128 </test> | 360 </div> |
129 <test> | 361 |
130 <repeat name="results"> | 362 <div class="select-menu-no-results">Nothing to show</div> |
131 <param name="software" value="cutadapt" /> | 363 </div> |
132 <param name="input_file" value="cutadapt.txt" /> | 364 |
133 </repeat> | 365 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> |
134 <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/> | 366 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> |
135 </test> | 367 |
136 <test> | 368 |
137 <repeat name="results"> | 369 </div> |
138 <param name="software" value="tophat" /> | 370 |
139 <param name="input_file" value="tophat_data.txt" /> | 371 <div class="select-menu-no-results">Nothing to show</div> |
140 </repeat> | 372 </div> |
141 <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/> | 373 |
142 </test> | 374 </div> |
143 <test> | 375 </div> |
144 <repeat name="results"> | 376 </div> |
145 <param name="software" value="bowtie2" /> | 377 |
146 <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" /> | 378 <div class="BtnGroup float-right"> |
147 </repeat> | 379 <a href="/EnginesOn/galaxy_tools/find/master" |
148 <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/> | 380 class="js-pjax-capture-input btn btn-sm BtnGroup-item" |
149 </test> | 381 data-pjax |
150 <test> | 382 data-hotkey="t"> |
151 <repeat name="results"> | 383 Find file |
152 <param name="software" value="featurecounts" /> | 384 </a> |
153 <param name="input_file" value="featurecounts_data.txt" /> | 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> |
154 </repeat> | 386 </div> |
155 <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/> | 387 <div class="breadcrumb js-zeroclipboard-target"> |
156 </test> | 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> |
157 <test> | 389 </div> |
158 <repeat name="results"> | 390 </div> |
159 <param name="software" value="picard" /> | 391 |
160 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" /> | 392 |
161 </repeat> | 393 <include-fragment class="commit-tease" src="/EnginesOn/galaxy_tools/contributors/master/tools/multiqc/multiqc.xml"> |
162 <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/> | 394 <div> |
163 </test> | 395 Fetching contributors… |
164 <test> | 396 </div> |
165 <repeat name="results"> | 397 |
166 <param name="software" value="htseq" /> | 398 <div class="commit-tease-contributors"> |
167 <param name="input_file" value="htseq_data.txt" /> | 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" /> |
168 </repeat> | 400 <span class="loader-error">Cannot retrieve contributors at this time</span> |
169 <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/> | 401 </div> |
170 </test> | 402 </include-fragment> |
171 <test> | 403 <div class="file"> |
172 <repeat name="results"> | 404 <div class="file-header"> |
173 <param name="software" value="rnastar_log" /> | 405 <div class="file-actions"> |
174 <param name="input_file" value="rnastar_log.txt" /> | 406 |
175 </repeat> | 407 <div class="BtnGroup"> |
176 <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/> | 408 <a href="/EnginesOn/galaxy_tools/raw/master/tools/multiqc/multiqc.xml" class="btn btn-sm BtnGroup-item" id="raw-url">Raw</a> |
177 </test> | 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> |
178 <test> | 410 <a href="/EnginesOn/galaxy_tools/commits/master/tools/multiqc/multiqc.xml" class="btn btn-sm BtnGroup-item" rel="nofollow">History</a> |
179 <repeat name="results"> | 411 </div> |
180 <param name="software" value="rnastar_counts" /> | 412 |
181 <param name="input_file" value="rnastar_counts.txt" /> | 413 |
182 </repeat> | 414 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" |
183 <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/> | 415 aria-label="You must be signed in to make or propose changes"> |
184 </test> | 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> |
185 <test> | 417 </button> |
186 <repeat name="results"> | 418 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" |
187 <param name="software" value="bismark" /> | 419 aria-label="You must be signed in to make or propose changes"> |
188 <param name="input_file" value="bismark_data.txt" /> | 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> |
189 </repeat> | 421 </button> |
190 <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/> | 422 </div> |
191 </test> | 423 |
192 <test> | 424 <div class="file-info"> |
193 <repeat name="results"> | 425 277 lines (263 sloc) |
194 <param name="software" value="samtools" /> | 426 <span class="file-info-divider"></span> |
195 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | 427 13.7 KB |
196 </repeat> | 428 </div> |
197 <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/> | 429 </div> |
198 </test> | 430 |
199 <test> | 431 |
200 <repeat name="results"> | 432 |
201 <param name="software" value="samtools_idxstats" /> | 433 <div itemprop="text" class="blob-wrapper data type-xml"> |
202 <param name="input_file" value="samtools_idxstats.txt" /> | 434 <table class="highlight tab-size js-file-line-container" data-tab-size="8"> |
203 </repeat> | 435 <tr> |
204 <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/> | 436 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> |
205 </test> | 437 <td id="LC1" class="blob-code blob-code-inner js-file-line"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@.0<span class="pl-pds">"</span></span>></td> |
206 <test> | 438 </tr> |
207 <repeat name="results"> | 439 <tr> |
208 <param name="software" value="fastqc" /> | 440 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> |
209 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | 441 <td id="LC2" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">description</span>>aggregate results from bioinformatics analyses into a single report</<span class="pl-ent">description</span>></td> |
210 </repeat> | 442 </tr> |
211 <repeat name="results"> | 443 <tr> |
212 <param name="software" value="cutadapt" /> | 444 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> |
213 <param name="input_file" value="cutadapt.txt" /> | 445 <td id="LC3" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">macros</span>></td> |
214 </repeat> | 446 </tr> |
215 <repeat name="results"> | 447 <tr> |
216 <param name="software" value="tophat" /> | 448 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> |
217 <param name="input_file" value="tophat_data.txt" /> | 449 <td id="LC4" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">token</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>1.0.0</<span class="pl-ent">token</span>></td> |
218 </repeat> | 450 </tr> |
219 <repeat name="results"> | 451 <tr> |
220 <param name="software" value="featurecounts" /> | 452 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> |
221 <param name="input_file" value="featurecounts_data.txt" /> | 453 <td id="LC5" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">macros</span>></td> |
222 </repeat> | 454 </tr> |
223 <repeat name="results"> | 455 <tr> |
224 <param name="software" value="picard" /> | 456 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> |
225 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" /> | 457 <td id="LC6" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirements</span>></td> |
226 </repeat> | 458 </tr> |
227 <repeat name="results"> | 459 <tr> |
228 <param name="software" value="bismark" /> | 460 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> |
229 <param name="input_file" value="bismark_data.txt" /> | 461 <td id="LC7" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>package<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>multiqc</<span class="pl-ent">requirement</span>></td> |
230 </repeat> | 462 </tr> |
231 <repeat name="results"> | 463 <tr> |
232 <param name="software" value="samtools" /> | 464 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> |
233 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | 465 <td id="LC8" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">requirements</span>></td> |
234 </repeat> | 466 </tr> |
235 <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/> | 467 <tr> |
236 </test> | 468 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> |
237 </tests> | 469 <td id="LC9" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">version_command</span>>@WRAPPER_VERSION@</<span class="pl-ent">version_command</span>></td> |
238 | 470 </tr> |
239 <help> | 471 <tr> |
240 **What it does** | 472 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> |
241 | 473 <td id="LC10" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">command</span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">"</span>aggressive<span class="pl-pds">"</span></span>></td> |
242 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. | 474 </tr> |
243 | 475 <tr> |
244 **Inputs** | 476 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> |
245 | 477 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds"><![CDATA[</span></span></td> |
246 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: | 478 </tr> |
247 | 479 <tr> |
248 - Fastqc | 480 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> |
249 - Cutadapt / Trim Galore! | 481 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s">mkdir multiqc_WDir &&</span></td> |
250 - Tophat2 | 482 </tr> |
251 - FeatureCounts | 483 <tr> |
252 - Samtools (stats, flagstat, dxstats) | 484 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> |
253 - Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics) | 485 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> |
254 - Bismark (Alignment report file) | 486 </tr> |
255 - Bowtie2 (Metrics file) | 487 <tr> |
256 - HTSeq-count ("no feature" file; although the "Assigned" metric is always 0) | 488 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> |
257 - RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab) | 489 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#for $i, $repeat in enumerate( $results )</span></td> |
258 | 490 </tr> |
259 ---- | 491 <tr> |
260 | 492 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> |
261 **Integrated by** | 493 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir multiqc_WDir/${repeat.software}_${i} &&</span></td> |
262 | 494 </tr> |
263 Cyril Monjeaud and Yvan Le Bras | 495 <tr> |
264 | 496 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> |
265 `EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility | 497 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> |
266 | 498 </tr> |
267 </help> | 499 <tr> |
268 <citations> | 500 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> |
269 <citation type="doi">10.1093/bioinformatics/btw354</citation> | 501 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if str($repeat.software) == "fastqc":</span></td> |
270 </citations> | 502 </tr> |
271 </tool> | 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 "fastqc_data.txt"</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_${k} &&</span></td> | |
514 </tr> | |
515 <tr> | |
516 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> | |
517 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &&</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) == "tophat":</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 "align_summary.txt"</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 $repeat.input_file:</span></td> | |
534 </tr> | |
535 <tr> | |
536 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> | |
537 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' &&</span></td> | |
538 </tr> | |
539 <tr> | |
540 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> | |
541 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
542 </tr> | |
543 <tr> | |
544 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> | |
545 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bowtie2":</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 'reads; of these;'</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 $repeat.input_file:</span></td> | |
554 </tr> | |
555 <tr> | |
556 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> | |
557 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td> | |
558 </tr> | |
559 <tr> | |
560 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> | |
561 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
562 </tr> | |
563 <tr> | |
564 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> | |
565 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "cutadapt":</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 'This is cutadapt'</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 $repeat.input_file:</span></td> | |
574 </tr> | |
575 <tr> | |
576 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> | |
577 <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td> | |
578 </tr> | |
579 <tr> | |
580 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> | |
581 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## replace header for old cutadapt release</span></td> | |
582 </tr> | |
583 <tr> | |
584 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> | |
585 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</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) == "featurecounts":</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 '.summary'</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 $file.metadata.column_names.find(',') != -1</span></td> | |
606 </tr> | |
607 <tr> | |
608 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> | |
609 <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> | |
610 </tr> | |
611 <tr> | |
612 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> | |
613 <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> | |
614 </tr> | |
615 <tr> | |
616 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> | |
617 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else</span></td> | |
618 </tr> | |
619 <tr> | |
620 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> | |
621 <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td> | |
622 </tr> | |
623 <tr> | |
624 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> | |
625 <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td> | |
626 </tr> | |
627 <tr> | |
628 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> | |
629 <td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
630 </tr> | |
631 <tr> | |
632 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> | |
633 <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bismark":</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 ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' &&</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) == "samtools":</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 'This file was produced by samtools stats'</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 ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</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) == "picard":</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 $repeat.input_file</span></td> | |
678 </tr> | |
679 <tr> | |
680 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> | |
681 <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> | |
682 </tr> | |
683 <tr> | |
684 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> | |
685 <td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
686 </tr> | |
687 <tr> | |
688 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> | |
689 <td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "samtools_idxstats":</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 "idxstats" 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 $repeat.input_file</span></td> | |
698 </tr> | |
699 <tr> | |
700 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> | |
701 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' &&</span></td> | |
702 </tr> | |
703 <tr> | |
704 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> | |
705 <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
706 </tr> | |
707 <tr> | |
708 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> | |
709 <td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "htseq":</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 "__too_low_aQual"</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 $repeat.input_file</span></td> | |
718 </tr> | |
719 <tr> | |
720 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> | |
721 <td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> | |
722 </tr> | |
723 <tr> | |
724 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> | |
725 <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
726 </tr> | |
727 <tr> | |
728 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> | |
729 <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_log":</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 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> | |
742 </tr> | |
743 <tr> | |
744 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> | |
745 <td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' &&</span></td> | |
746 </tr> | |
747 <tr> | |
748 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> | |
749 <td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td> | |
750 </tr> | |
751 <tr> | |
752 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> | |
753 <td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_counts":</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 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td> | |
766 </tr> | |
767 <tr> | |
768 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> | |
769 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' &&</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">]]></span></span></<span class="pl-ent">command</span>></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"> <<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span> <span class="pl-e">title</span>=<span class="pl-s"><span class="pl-pds">"</span>Results<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">"</span>1<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Software name<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Which tool was used generate logs?<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span>>FastQC</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span>>Cutadapt/Trim Galore!</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span>>Tophat2</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span>>FeatureCounts (Summary file)</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span>>Samtools (Stats, Flagstat)</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span>>Samtools (Idxstats)</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span>>Picard</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span>>Bismark</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span>>Bowtie2</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span>>HTSeq-Count</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span>>RNA STAR (log)</<span class="pl-ent">option</span>></td> | |
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"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span>>RNA STAR (reads per gene)</<span class="pl-ent">option</span>></td> | |
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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt, tabular<span class="pl-pds">"</span></span> <span class="pl-e">multiple</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Result file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Select input datasets<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>boolean<span class="pl-pds">"</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">checked</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Save log file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Save the multiQC log file to the history. This is mostly useful for debugging purposes.<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">outputs</span>></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"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>html<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_report.html<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Webpage<span class="pl-pds">"</span></span> /></td> | |
882 </tr> | |
883 <tr> | |
884 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> | |
885 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_data/multiqc.log<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Log<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">filter</span>>saveLog</<span class="pl-ent">filter</span>></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"> </<span class="pl-ent">data</span>></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"> </<span class="pl-ent">outputs</span>></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"> <<span class="pl-ent">tests</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span>/></td> | |
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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>log_fastqc.txt<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc_2.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_cutadapt.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_tophat.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2SE1.txt,bowtie2SE2.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bowtie2SE.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_featurecounts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_picard.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>10000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_htseq.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_log.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_counts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bismark.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools_idxstats.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></td> | |
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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></td> | |
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"> </<span class="pl-ent">repeat</span>></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"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_all.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>5000<span class="pl-pds">"</span></span>/></td> | |
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"> </<span class="pl-ent">test</span>></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"> </<span class="pl-ent">tests</span>></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"> <<span class="pl-ent">help</span>><span class="pl-s"><span class="pl-pds"><![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'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 ("no feature" file; although the "Assigned" 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 &lt;http://engineson.fr/&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">]]></span></span></<span class="pl-ent">help</span>></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"> <<span class="pl-ent">citations</span>></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"> <<span class="pl-ent">citation</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>doi<span class="pl-pds">"</span></span>>10.1093/bioinformatics/btw354</<span class="pl-ent">citation</span>></td> | |
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"> </<span class="pl-ent">citations</span>></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"></<span class="pl-ent">tool</span>></td> | |
1539 </tr> | |
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1541 | |
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