comparison VAP.xml @ 14:7d1f86b4718d draft

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author johnheap
date Mon, 03 Jun 2019 15:56:10 -0400
parents 6450a72e8f6b
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13:8c210b4ad003 14:7d1f86b4718d
1 <tool id="VAP" name="VAPPER" version="1.1.0">
2 <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description>
3 <requirements>
4 <requirement type="package" version="1.2.10">velvet</requirement>
5 <requirement type="package" version="3.1b2">HMMER</requirement>
6 <requirement type="package" version="2.2.6">bowtie2</requirement>
7 <requirement type="package" version="1.6">samtools</requirement>
8 <requirement type="package" version="2.2.1">cufflinks</requirement>
9 <requirement type="package" version="2.7.1">blast</requirement>
10 <requirement type="package" version="6.6.0.0">EMBOSS</requirement>
11 <requirement type="package" version="0.8.0">seaborn</requirement>
12 </requirements>
1 13
2 14
15 <command interpreter="python" detect_errors="exit_code">
16 #if $TrypType.species == "Trypanosoma congolense":
17 #if $TrypType.GT.analysis == "Genomic":
18 #if $TrypType.GT.contigs.preassem == "Contig available":
19 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
20 Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path
21 #else
22 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
23 Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path
24 #end if
25 #else
26 <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 -->
27 Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path
28 #end if
29 #else
30 #if $TrypType.GT.analysis == "Transcriptomic":
31 Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path
32 #else
33 #if $TrypType.contigs.preassem == "Contig available":
34 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
35 Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path
36 #else
37 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
38 Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path
39 #end if
40 #end if
41 #end if
3 42
43 </command>
4 44
45 <inputs>
46 <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" />
47 <conditional name = "TrypType">
48 <param name = "species" type = 'select' label="Select Species">
49 <option value = "Trypanosoma congolense" selected="true"></option>
50 <option value = "Trypanosoma vivax"></option>
51 </param>
52 <when value = "Trypanosoma congolense">
53 <conditional name = "GT">
54 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">
55 <option value = "Genomic" selected = "true"></option>
56 <option value = "Transcriptomic"></option>
57 </param>
58 <when value = "Genomic">
59 <conditional name = "contigs">
60 <param name = "preassem" type = "select" label = "Contig file available?">
61 <option value = "Full assembly" selected = "true"></option>
62 <option value = "Contig available"></option>
63 </param>
64 <when value = "Full assembly">
65 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
66 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
67 <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param>
68 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
69 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
70 </when>
71 <when value = "Contig available">
72 <param name="contig" type="data" format="fasta" label="Contig file"/>
73 </when>
74 </conditional>
75 </when>
76 <when value = "Transcriptomic">
77 <param name = "strain" type="select" label = "Select Reference Strain">
78 <option value = "Tc148"></option>
79 <option value = "IL3000"></option>
80 </param>
81 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
82 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
83 </when>
84 </conditional>
85 </when>
86 <when value="Trypanosoma vivax">
87 <conditional name = "GT">
88 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">
89 <option value = "Genomic" selected = "true"></option>
90 <option value = "Transcriptomic"></option>
91 </param>
92 <when value = "Genomic">
93 <conditional name = "contigs">
94 <param name = "preassem" type = "select" label = "Contig file available?">
95 <option value = "Full assembly" selected = "true"></option>
96 <option value = "Contig available"></option>
97 </param>
98 <when value = "Full assembly">
99 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
100 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
101 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
102 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
103 </when>
104 <when value = "Contig available">
105 <param name="contig" type="data" format="fasta" label="Contig file"/>
106 </when>
107 </conditional>
108 </when>
109 <when value = "Transcriptomic">
110 <param name = "vtreference" type="data" format="fasta" label = "Reference File"/>
111 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
112 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
113 </when>
114 </conditional>
115 </when>
116 </conditional>
5 117
118 <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" />
119 </inputs>
6 120
7 <!DOCTYPE html> 121 <outputs>
8 <html lang="en"> 122 <data format="html" name = "html_file" label = "${xname.value}_html"/>
9 <head> 123 </outputs>
10 <meta charset="utf-8"> 124 <tests>
11 <link rel="dns-prefetch" href="https://github.githubassets.com"> 125 <test>
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> 126 <param name = "xname" value = "Test"/>
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> 127 <conditional name = "TrypType">
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> 128 <param name = "species" value = "Trypanosoma congolense"/>
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> 129 </conditional>
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> 130 <conditional name = "GT">
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> 131 <param name = "analysis" value = "Genomic"/>
132 </conditional>
133 <conditional name = "contigs">
134 <param name = "preassem" value = "Contig available"/>
135 <param name="contig" value = "Test.fa"/>
136 </conditional>
137 <param name = "P" value = 'PDF_No'/>
138 <output name = "html_file" file = 'Test_html' ftype = 'html'/>
139 </test>
140 </tests>
141 </tool>
18 142
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176 <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li>
177 </ul>
178
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
180 <li class="edge-item-fix"><a href="/customer-stories" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
181 <li class="edge-item-fix"><a href="/security" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
182 </ul>
183 </div>
184 </details>
185 </li>
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
187 <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a>
188 </li>
189
190 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
191 <details class="HeaderMenu-details details-overlay details-reset width-full">
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
193 Explore
194 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
195 <path d="M1,1l6.2,6L13,1"></path>
196 </svg>
197 </summary>
198
199 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
200 <ul class="list-style-none mb-3">
201 <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
202 </ul>
203
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn &amp; contribute</h4>
205 <ul class="list-style-none mb-3">
206 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li>
207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li>
208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li>
209 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li>
210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li>
211 </ul>
212
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
214 <ul class="list-style-none mb-0">
215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li>
216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li>
217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li>
218 </ul>
219 </div>
220 </details>
221 </li>
222
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a>
225 </li>
226
227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
228 <details class="HeaderMenu-details details-overlay details-reset width-full">
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
230 Pricing
231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
232 <path d="M1,1l6.2,6L13,1"></path>
233 </svg>
234 </summary>
235
236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
238
239 <ul class="list-style-none mb-3">
240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li>
241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li>
242 </ul>
243
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
246 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
247 </ul>
248 </div>
249 </details>
250 </li>
251 </ul>
252 </nav>
253
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
255 <div class="d-lg-flex mb-3 mb-lg-0">
256 <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to"
257 role="combobox"
258 aria-owns="jump-to-results"
259 aria-label="Search or jump to"
260 aria-haspopup="listbox"
261 aria-expanded="false"
262 >
263 <div class="position-relative">
264 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
265 <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container">
266 <input type="text"
267 class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable"
268 data-hotkey="s,/"
269 name="q"
270 value=""
271 placeholder="Search"
272 data-unscoped-placeholder="Search GitHub"
273 data-scoped-placeholder="Search"
274 autocapitalize="off"
275 aria-autocomplete="list"
276 aria-controls="jump-to-results"
277 aria-label="Search"
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=KTCloZOsmcJnQG8+9Rpx1bhv3g0Y6RphAwXNxB0AQyG1y/I19pdeBJolo4nekuHBWhvAt65+3d/8rLCh6xmeUw=="
279 spellcheck="false"
280 autocomplete="off"
281 >
282 <input type="hidden" class="js-site-search-type-field" name="type" >
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
284
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
286
287 <ul class="d-none js-jump-to-suggestions-template-container">
288
289
290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><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>
295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
296 </div>
297
298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
299
300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
301 </div>
302
303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
305 In this repository
306 </span>
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
308 All GitHub
309 </span>
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
311 </div>
312
313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
314 Jump to
315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
316 </div>
317 </a>
318 </li>
319
320 </ul>
321
322 <ul class="d-none js-jump-to-no-results-template-container">
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
324 <span class="text-gray">No suggested jump to results</span>
325 </li>
326 </ul>
327
328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
329
330
331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><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>
336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
337 </div>
338
339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
340
341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
342 </div>
343
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
346 In this repository
347 </span>
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
349 All GitHub
350 </span>
351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
352 </div>
353
354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
355 Jump to
356 <span class="d-inline-block ml-1 v-align-middle">↵</span>
357 </div>
358 </a>
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360
361
362
363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><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>
368 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
372
373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
374 </div>
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377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
378 In this repository
379 </span>
380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
381 All GitHub
382 </span>
383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
384 </div>
385
386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
387 Jump to
388 <span class="d-inline-block ml-1 v-align-middle">↵</span>
389 </div>
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393
394 </ul>
395
396 </div>
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401 </div>
402
403 <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;99EF:3DF4:A496E:120BBA:5CF562BE&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/VAP.xml&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4f690ef143e2ef8459c43b1cbf0fd9a9eec10f2a80477c079b3de11e63ff5f09" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FVAP.xml">
404 Sign&nbsp;in
405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;99EF:3DF4:A496E:120BBA:5CF562BE&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/VAP.xml&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="ec8ff730fd1d25dbc45baf1260ca99d2d34f31dc8b2a02c77ee87f2053979769" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
406 Sign&nbsp;up
407 </a> </div>
408 </div>
409 </div>
410 </header>
411
412 </div>
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704 <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><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>
705 </button>
706 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
707 aria-label="You must be signed in to make or propose changes">
708 <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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>
709 </button>
710 </div>
711 </div>
712 </div>
713
714
715
716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-xml ">
717
718 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
719 <tr>
720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
721 <td id="LC1" class="blob-code blob-code-inner js-file-line">&lt;<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>VAP<span class="pl-pds">&quot;</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>VAPPER<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1.1.0<span class="pl-pds">&quot;</span></span>&gt;</td>
722 </tr>
723 <tr>
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">description</span>&gt;is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate&lt;/<span class="pl-ent">description</span>&gt;</td>
726 </tr>
727 <tr>
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
729 <td id="LC3" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirements</span>&gt;</td>
730 </tr>
731 <tr>
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
733 <td id="LC4" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1.2.10<span class="pl-pds">&quot;</span></span>&gt;velvet&lt;/<span class="pl-ent">requirement</span>&gt;</td>
734 </tr>
735 <tr>
736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>3.1b2<span class="pl-pds">&quot;</span></span>&gt;HMMER&lt;/<span class="pl-ent">requirement</span>&gt;</td>
738 </tr>
739 <tr>
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>2.2.6<span class="pl-pds">&quot;</span></span>&gt;bowtie2&lt;/<span class="pl-ent">requirement</span>&gt;</td>
742 </tr>
743 <tr>
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1.6<span class="pl-pds">&quot;</span></span>&gt;samtools&lt;/<span class="pl-ent">requirement</span>&gt;</td>
746 </tr>
747 <tr>
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>2.2.1<span class="pl-pds">&quot;</span></span>&gt;cufflinks&lt;/<span class="pl-ent">requirement</span>&gt;</td>
750 </tr>
751 <tr>
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>2.7.1<span class="pl-pds">&quot;</span></span>&gt;blast&lt;/<span class="pl-ent">requirement</span>&gt;</td>
754 </tr>
755 <tr>
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>6.6.0.0<span class="pl-pds">&quot;</span></span>&gt;EMBOSS&lt;/<span class="pl-ent">requirement</span>&gt;</td>
758 </tr>
759 <tr>
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>package<span class="pl-pds">&quot;</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>0.8.0<span class="pl-pds">&quot;</span></span>&gt;seaborn&lt;/<span class="pl-ent">requirement</span>&gt;</td>
762 </tr>
763 <tr>
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
765 <td id="LC12" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">requirements</span>&gt;</td>
766 </tr>
767 <tr>
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
769 <td id="LC13" class="blob-code blob-code-inner js-file-line">
770 </td>
771 </tr>
772 <tr>
773 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
774 <td id="LC14" class="blob-code blob-code-inner js-file-line">
775 </td>
776 </tr>
777 <tr>
778 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
779 <td id="LC15" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">command</span> <span class="pl-e">interpreter</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>python<span class="pl-pds">&quot;</span></span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>exit_code<span class="pl-pds">&quot;</span></span>&gt;</td>
780 </tr>
781 <tr>
782 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
783 <td id="LC16" class="blob-code blob-code-inner js-file-line"> #if $TrypType.species == &quot;Trypanosoma congolense&quot;:</td>
784 </tr>
785 <tr>
786 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
787 <td id="LC17" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.analysis == &quot;Genomic&quot;:</td>
788 </tr>
789 <tr>
790 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
791 <td id="LC18" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.contigs.preassem == &quot;Contig available&quot;:</td>
792 </tr>
793 <tr>
794 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
795 <td id="LC19" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">&lt;!--</span> name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 <span class="pl-c">--&gt;</span></span></td>
796 </tr>
797 <tr>
798 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
799 <td id="LC20" class="blob-code blob-code-inner js-file-line"> Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path</td>
800 </tr>
801 <tr>
802 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
803 <td id="LC21" class="blob-code blob-code-inner js-file-line"> #else</td>
804 </tr>
805 <tr>
806 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
807 <td id="LC22" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">&lt;!--</span> name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 <span class="pl-c">--&gt;</span></span></td>
808 </tr>
809 <tr>
810 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
811 <td id="LC23" class="blob-code blob-code-inner js-file-line"> Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path</td>
812 </tr>
813 <tr>
814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
815 <td id="LC24" class="blob-code blob-code-inner js-file-line"> #end if</td>
816 </tr>
817 <tr>
818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
819 <td id="LC25" class="blob-code blob-code-inner js-file-line"> #else</td>
820 </tr>
821 <tr>
822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
823 <td id="LC26" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">&lt;!--</span> name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 <span class="pl-c">--&gt;</span></span></td>
824 </tr>
825 <tr>
826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
827 <td id="LC27" class="blob-code blob-code-inner js-file-line"> Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path</td>
828 </tr>
829 <tr>
830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
831 <td id="LC28" class="blob-code blob-code-inner js-file-line"> #end if</td>
832 </tr>
833 <tr>
834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
835 <td id="LC29" class="blob-code blob-code-inner js-file-line"> #else</td>
836 </tr>
837 <tr>
838 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
839 <td id="LC30" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.analysis == &quot;Transcriptomic&quot;:</td>
840 </tr>
841 <tr>
842 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
843 <td id="LC31" class="blob-code blob-code-inner js-file-line"> Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path</td>
844 </tr>
845 <tr>
846 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
847 <td id="LC32" class="blob-code blob-code-inner js-file-line"> #else</td>
848 </tr>
849 <tr>
850 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
851 <td id="LC33" class="blob-code blob-code-inner js-file-line"> #if $TrypType.contigs.preassem == &quot;Contig available&quot;:</td>
852 </tr>
853 <tr>
854 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
855 <td id="LC34" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">&lt;!--</span> name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 <span class="pl-c">--&gt;</span></span></td>
856 </tr>
857 <tr>
858 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
859 <td id="LC35" class="blob-code blob-code-inner js-file-line"> Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path</td>
860 </tr>
861 <tr>
862 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
863 <td id="LC36" class="blob-code blob-code-inner js-file-line"> #else</td>
864 </tr>
865 <tr>
866 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
867 <td id="LC37" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">&lt;!--</span> name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 <span class="pl-c">--&gt;</span></span></td>
868 </tr>
869 <tr>
870 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
871 <td id="LC38" class="blob-code blob-code-inner js-file-line"> Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path</td>
872 </tr>
873 <tr>
874 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
875 <td id="LC39" class="blob-code blob-code-inner js-file-line"> #end if</td>
876 </tr>
877 <tr>
878 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
879 <td id="LC40" class="blob-code blob-code-inner js-file-line"> #end if </td>
880 </tr>
881 <tr>
882 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
883 <td id="LC41" class="blob-code blob-code-inner js-file-line"> #end if</td>
884 </tr>
885 <tr>
886 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
887 <td id="LC42" class="blob-code blob-code-inner js-file-line">
888 </td>
889 </tr>
890 <tr>
891 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
892 <td id="LC43" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">command</span>&gt;</td>
893 </tr>
894 <tr>
895 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
896 <td id="LC44" class="blob-code blob-code-inner js-file-line">
897 </td>
898 </tr>
899 <tr>
900 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
901 <td id="LC45" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">inputs</span>&gt;</td>
902 </tr>
903 <tr>
904 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
905 <td id="LC46" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>xname<span class="pl-pds">&quot;</span></span> size = <span class="pl-s"><span class="pl-pds">&quot;</span>30<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>text<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Test<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Prefix Name<span class="pl-pds">&quot;</span></span> /&gt;</td>
906 </tr>
907 <tr>
908 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
909 <td id="LC47" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>TrypType<span class="pl-pds">&quot;</span></span>&gt;</td>
910 </tr>
911 <tr>
912 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
913 <td id="LC48" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>species<span class="pl-pds">&quot;</span></span> type = <span class="pl-s"><span class="pl-pds">&#39;</span>select<span class="pl-pds">&#39;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Select Species<span class="pl-pds">&quot;</span></span>&gt;</td>
914 </tr>
915 <tr>
916 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
917 <td id="LC49" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Trypanosoma congolense<span class="pl-pds">&quot;</span></span> <span class="pl-e">selected</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
918 </tr>
919 <tr>
920 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
921 <td id="LC50" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Trypanosoma vivax<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
922 </tr>
923 <tr>
924 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
925 <td id="LC51" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
926 </tr>
927 <tr>
928 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
929 <td id="LC52" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Trypanosoma congolense<span class="pl-pds">&quot;</span></span>&gt;</td>
930 </tr>
931 <tr>
932 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
933 <td id="LC53" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>GT<span class="pl-pds">&quot;</span></span>&gt;</td>
934 </tr>
935 <tr>
936 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
937 <td id="LC54" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>analysis<span class="pl-pds">&quot;</span></span> type = <span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic or Transcriptomic Analysis?<span class="pl-pds">&quot;</span></span>&gt;</td>
938 </tr>
939 <tr>
940 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
941 <td id="LC55" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic<span class="pl-pds">&quot;</span></span> selected = <span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
942 </tr>
943 <tr>
944 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
945 <td id="LC56" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Transcriptomic<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
946 </tr>
947 <tr>
948 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
949 <td id="LC57" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
950 </tr>
951 <tr>
952 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
953 <td id="LC58" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic<span class="pl-pds">&quot;</span></span>&gt;</td>
954 </tr>
955 <tr>
956 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
957 <td id="LC59" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>contigs<span class="pl-pds">&quot;</span></span>&gt;</td>
958 </tr>
959 <tr>
960 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
961 <td id="LC60" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>preassem<span class="pl-pds">&quot;</span></span> type = <span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig file available?<span class="pl-pds">&quot;</span></span>&gt;</td>
962 </tr>
963 <tr>
964 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
965 <td id="LC61" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Full assembly<span class="pl-pds">&quot;</span></span> selected = <span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
966 </tr>
967 <tr>
968 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
969 <td id="LC62" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig available<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
970 </tr>
971 <tr>
972 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
973 <td id="LC63" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
974 </tr>
975 <tr>
976 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
977 <td id="LC64" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Full assembly<span class="pl-pds">&quot;</span></span>&gt;</td>
978 </tr>
979 <tr>
980 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
981 <td id="LC65" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>kmers<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>integer<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>65<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>31<span class="pl-pds">&quot;</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>99<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Specify kmers<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">param</span>&gt;</td>
982 </tr>
983 <tr>
984 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
985 <td id="LC66" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>inslen<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>integer<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>400<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1<span class="pl-pds">&quot;</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>999<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Insert length<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">param</span>&gt;</td>
986 </tr>
987 <tr>
988 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
989 <td id="LC67" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>covcut<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>integer<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>5<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1<span class="pl-pds">&quot;</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>999<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Coverage cut off<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">param</span>&gt;</td>
990 </tr>
991 <tr>
992 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
993 <td id="LC68" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>forward<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Forward NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
994 </tr>
995 <tr>
996 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
997 <td id="LC69" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reverse<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Reverse NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
998 </tr>
999 <tr>
1000 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
1001 <td id="LC70" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1002 </tr>
1003 <tr>
1004 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
1005 <td id="LC71" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig available<span class="pl-pds">&quot;</span></span>&gt;</td>
1006 </tr>
1007 <tr>
1008 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
1009 <td id="LC72" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>contig<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fasta<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Contig file<span class="pl-pds">&quot;</span></span>/&gt;</td>
1010 </tr>
1011 <tr>
1012 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
1013 <td id="LC73" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1014 </tr>
1015 <tr>
1016 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
1017 <td id="LC74" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1018 </tr>
1019 <tr>
1020 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
1021 <td id="LC75" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1022 </tr>
1023 <tr>
1024 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
1025 <td id="LC76" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Transcriptomic<span class="pl-pds">&quot;</span></span>&gt;</td>
1026 </tr>
1027 <tr>
1028 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
1029 <td id="LC77" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>strain<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Select Reference Strain<span class="pl-pds">&quot;</span></span>&gt;</td>
1030 </tr>
1031 <tr>
1032 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
1033 <td id="LC78" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1034 </tr>
1035 <tr>
1036 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
1037 <td id="LC79" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1038 </tr>
1039 <tr>
1040 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
1041 <td id="LC80" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
1042 </tr>
1043 <tr>
1044 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
1045 <td id="LC81" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>forward<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Forward NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1046 </tr>
1047 <tr>
1048 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
1049 <td id="LC82" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reverse<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Reverse NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1050 </tr>
1051 <tr>
1052 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
1053 <td id="LC83" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1054 </tr>
1055 <tr>
1056 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
1057 <td id="LC84" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1058 </tr>
1059 <tr>
1060 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
1061 <td id="LC85" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1062 </tr>
1063 <tr>
1064 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
1065 <td id="LC86" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Trypanosoma vivax<span class="pl-pds">&quot;</span></span>&gt;</td>
1066 </tr>
1067 <tr>
1068 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
1069 <td id="LC87" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>GT<span class="pl-pds">&quot;</span></span>&gt;</td>
1070 </tr>
1071 <tr>
1072 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
1073 <td id="LC88" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>analysis<span class="pl-pds">&quot;</span></span> type = <span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic or Transcriptomic Analysis?<span class="pl-pds">&quot;</span></span>&gt;</td>
1074 </tr>
1075 <tr>
1076 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
1077 <td id="LC89" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic<span class="pl-pds">&quot;</span></span> selected = <span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1078 </tr>
1079 <tr>
1080 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
1081 <td id="LC90" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Transcriptomic<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1082 </tr>
1083 <tr>
1084 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
1085 <td id="LC91" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
1086 </tr>
1087 <tr>
1088 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
1089 <td id="LC92" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic<span class="pl-pds">&quot;</span></span>&gt;</td>
1090 </tr>
1091 <tr>
1092 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
1093 <td id="LC93" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>contigs<span class="pl-pds">&quot;</span></span>&gt;</td>
1094 </tr>
1095 <tr>
1096 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
1097 <td id="LC94" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>preassem<span class="pl-pds">&quot;</span></span> type = <span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig file available?<span class="pl-pds">&quot;</span></span>&gt;</td>
1098 </tr>
1099 <tr>
1100 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
1101 <td id="LC95" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Full assembly<span class="pl-pds">&quot;</span></span> selected = <span class="pl-s"><span class="pl-pds">&quot;</span>true<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1102 </tr>
1103 <tr>
1104 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
1105 <td id="LC96" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig available<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">option</span>&gt;</td>
1106 </tr>
1107 <tr>
1108 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
1109 <td id="LC97" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
1110 </tr>
1111 <tr>
1112 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
1113 <td id="LC98" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Full assembly<span class="pl-pds">&quot;</span></span>&gt;</td>
1114 </tr>
1115 <tr>
1116 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
1117 <td id="LC99" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>kmers<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>integer<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>65<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>31<span class="pl-pds">&quot;</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>99<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Specify kmers<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">param</span>&gt;</td>
1118 </tr>
1119 <tr>
1120 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
1121 <td id="LC100" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>inslen<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>integer<span class="pl-pds">&quot;</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>400<span class="pl-pds">&quot;</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>1<span class="pl-pds">&quot;</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>999<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Insert length<span class="pl-pds">&quot;</span></span>&gt;&lt;/<span class="pl-ent">param</span>&gt;</td>
1122 </tr>
1123 <tr>
1124 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
1125 <td id="LC101" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>forward<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Forward NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1126 </tr>
1127 <tr>
1128 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
1129 <td id="LC102" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reverse<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Reverse NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1130 </tr>
1131 <tr>
1132 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
1133 <td id="LC103" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1134 </tr>
1135 <tr>
1136 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
1137 <td id="LC104" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig available<span class="pl-pds">&quot;</span></span>&gt;</td>
1138 </tr>
1139 <tr>
1140 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
1141 <td id="LC105" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>contig<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fasta<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Contig file<span class="pl-pds">&quot;</span></span>/&gt;</td>
1142 </tr>
1143 <tr>
1144 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
1145 <td id="LC106" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1146 </tr>
1147 <tr>
1148 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
1149 <td id="LC107" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1150 </tr>
1151 <tr>
1152 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
1153 <td id="LC108" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt; </td>
1154 </tr>
1155 <tr>
1156 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
1157 <td id="LC109" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Transcriptomic<span class="pl-pds">&quot;</span></span>&gt;</td>
1158 </tr>
1159 <tr>
1160 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
1161 <td id="LC110" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>vtreference<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fasta<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>Reference File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1162 </tr>
1163 <tr>
1164 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
1165 <td id="LC111" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>forward<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Forward NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1166 </tr>
1167 <tr>
1168 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
1169 <td id="LC112" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reverse<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fastq<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Reverse NGS Read File<span class="pl-pds">&quot;</span></span>/&gt;</td>
1170 </tr>
1171 <tr>
1172 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
1173 <td id="LC113" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
1174 </tr>
1175 <tr>
1176 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
1177 <td id="LC114" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1178 </tr>
1179 <tr>
1180 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
1181 <td id="LC115" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt; </td>
1182 </tr>
1183 <tr>
1184 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
1185 <td id="LC116" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1186 </tr>
1187 <tr>
1188 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
1189 <td id="LC117" class="blob-code blob-code-inner js-file-line">
1190 </td>
1191 </tr>
1192 <tr>
1193 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
1194 <td id="LC118" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>P<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>boolean<span class="pl-pds">&quot;</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">&#39;</span>PDF_No<span class="pl-pds">&#39;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Export PDF of figures<span class="pl-pds">&quot;</span></span> /&gt;</td>
1195 </tr>
1196 <tr>
1197 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
1198 <td id="LC119" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">inputs</span>&gt;</td>
1199 </tr>
1200 <tr>
1201 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
1202 <td id="LC120" class="blob-code blob-code-inner js-file-line">
1203 </td>
1204 </tr>
1205 <tr>
1206 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
1207 <td id="LC121" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">outputs</span>&gt;</td>
1208 </tr>
1209 <tr>
1210 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
1211 <td id="LC122" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>html<span class="pl-pds">&quot;</span></span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> label = <span class="pl-s"><span class="pl-pds">&quot;</span>${xname.value}_html<span class="pl-pds">&quot;</span></span>/&gt;</td>
1212 </tr>
1213 <tr>
1214 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
1215 <td id="LC123" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">outputs</span>&gt;</td>
1216 </tr>
1217 <tr>
1218 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
1219 <td id="LC124" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">tests</span>&gt;</td>
1220 </tr>
1221 <tr>
1222 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
1223 <td id="LC125" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">test</span>&gt;</td>
1224 </tr>
1225 <tr>
1226 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
1227 <td id="LC126" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>xname<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Test<span class="pl-pds">&quot;</span></span>/&gt;</td>
1228 </tr>
1229 <tr>
1230 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
1231 <td id="LC127" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>TrypType<span class="pl-pds">&quot;</span></span>&gt;</td>
1232 </tr>
1233 <tr>
1234 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
1235 <td id="LC128" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>species<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Trypanosoma congolense<span class="pl-pds">&quot;</span></span>/&gt;</td>
1236 </tr>
1237 <tr>
1238 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
1239 <td id="LC129" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1240 </tr>
1241 <tr>
1242 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
1243 <td id="LC130" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>GT<span class="pl-pds">&quot;</span></span>&gt;</td>
1244 </tr>
1245 <tr>
1246 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
1247 <td id="LC131" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>analysis<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Genomic<span class="pl-pds">&quot;</span></span>/&gt;</td>
1248 </tr>
1249 <tr>
1250 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
1251 <td id="LC132" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1252 </tr>
1253 <tr>
1254 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
1255 <td id="LC133" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>contigs<span class="pl-pds">&quot;</span></span>&gt;</td>
1256 </tr>
1257 <tr>
1258 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
1259 <td id="LC134" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>preassem<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Contig available<span class="pl-pds">&quot;</span></span>/&gt;</td>
1260 </tr>
1261 <tr>
1262 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
1263 <td id="LC135" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>contig<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&quot;</span>Test.fa<span class="pl-pds">&quot;</span></span>/&gt;</td>
1264 </tr>
1265 <tr>
1266 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
1267 <td id="LC136" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
1268 </tr>
1269 <tr>
1270 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
1271 <td id="LC137" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>P<span class="pl-pds">&quot;</span></span> value = <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_No<span class="pl-pds">&#39;</span></span>/&gt;</td>
1272 </tr>
1273 <tr>
1274 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
1275 <td id="LC138" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">output</span> name = <span class="pl-s"><span class="pl-pds">&quot;</span>html_file<span class="pl-pds">&quot;</span></span> file = <span class="pl-s"><span class="pl-pds">&#39;</span>Test_html<span class="pl-pds">&#39;</span></span> ftype = <span class="pl-s"><span class="pl-pds">&#39;</span>html<span class="pl-pds">&#39;</span></span>/&gt;</td>
1276 </tr>
1277 <tr>
1278 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
1279 <td id="LC139" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">test</span>&gt;</td>
1280 </tr>
1281 <tr>
1282 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
1283 <td id="LC140" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">tests</span>&gt;</td>
1284 </tr>
1285 <tr>
1286 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
1287 <td id="LC141" class="blob-code blob-code-inner js-file-line">&lt;/<span class="pl-ent">tool</span>&gt;</td>
1288 </tr>
1289 <tr>
1290 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
1291 <td id="LC142" class="blob-code blob-code-inner js-file-line">
1292 </td>
1293 </tr>
1294 </table>
1295
1296 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
1297 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
1298 <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
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1301 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
1302 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
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1361 </div>
1362 <div class="d-flex flex-justify-center pb-6">
1363 <span class="f6 text-gray-light"></span>
1364 </div>
1365 </div>
1366
1367
1368
1369 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
1370 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
1371 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
1372 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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 1.48L7.48 8z"/></svg>
1373 </button>
1374 You can’t perform that action at this time.
1375 </div>
1376
1377
1378 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
1379 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
1380
1381 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
1382
1383
1384
1385 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
1386 >
1387 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
1388 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
1389 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
1390 </div>
1391 <template id="site-details-dialog">
1392 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
1393 <summary role="button" aria-label="Close dialog"></summary>
1394 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
1395 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
1396 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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 1.48L7.48 8z"/></svg>
1397 </button>
1398 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
1399 </details-dialog>
1400 </details>
1401 </template>
1402
1403 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
1404 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
1405 </div>
1406 </div>
1407
1408 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
1409
1410 </body>
1411 </html>
1412