Mercurial > repos > johnheap > vapper
comparison VAP.xml @ 14:7d1f86b4718d draft
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author | johnheap |
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date | Mon, 03 Jun 2019 15:56:10 -0400 |
parents | 6450a72e8f6b |
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13:8c210b4ad003 | 14:7d1f86b4718d |
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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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167 <ul class="list-style-none f5 pb-3"> | |
168 <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li> | |
169 <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li> | |
170 <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li> | |
171 <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a> | |
172 <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a> | |
173 <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li> | |
174 <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li> | |
175 <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li> | |
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">→</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">→</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">→</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 & 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">→</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">→</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">→</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="✓" /> | |
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> | |
359 </li> | |
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> | |
369 </div> | |
370 | |
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> | |
375 | |
376 <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"> | |
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 | |
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646 </span> | |
647 <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0"> | |
648 <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">VAP.xml</strong> | |
649 </h2> | |
650 | |
651 <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block"> | |
652 <a href="/johnheap/VAPPER-Galaxy/find/master" | |
653 class="js-pjax-capture-input btn btn-sm BtnGroup-item" | |
654 data-pjax | |
655 data-hotkey="t"> | |
656 Find file | |
657 </a> | |
658 <clipboard-copy value="VAP.xml" class="btn btn-sm BtnGroup-item"> | |
659 Copy path | |
660 </clipboard-copy> | |
661 </div> | |
662 </div> | |
663 | |
664 | |
665 | |
666 <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/VAP.xml" class="Box Box--condensed commit-loader"> | |
667 <div class="Box-body bg-blue-light f6"> | |
668 Fetching contributors… | |
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670 | |
671 <div class="Box-body d-flex flex-items-center" > | |
672 <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" /> | |
673 <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span> | |
674 </div> | |
675 </include-fragment> | |
676 | |
677 | |
678 | |
679 | |
680 | |
681 <div class="Box mt-3 position-relative"> | |
682 | |
683 <div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center"> | |
684 | |
685 <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0"> | |
686 143 lines (135 sloc) | |
687 <span class="file-info-divider"></span> | |
688 7.93 KB | |
689 </div> | |
690 | |
691 <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between"> | |
692 | |
693 <div class="BtnGroup"> | |
694 <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/VAP.xml">Raw</a> | |
695 <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/VAP.xml">Blame</a> | |
696 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/VAP.xml">History</a> | |
697 </div> | |
698 | |
699 | |
700 <div> | |
701 | |
702 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" | |
703 aria-label="You must be signed in to make or propose changes"> | |
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"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>VAP<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>VAPPER<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>1.1.0<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">description</span>>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</<span class="pl-ent">description</span>></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"> <<span class="pl-ent">requirements</span>></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"> <<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>1.2.10<span class="pl-pds">"</span></span>>velvet</<span class="pl-ent">requirement</span>></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"> <<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>3.1b2<span class="pl-pds">"</span></span>>HMMER</<span class="pl-ent">requirement</span>></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"> <<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>2.2.6<span class="pl-pds">"</span></span>>bowtie2</<span class="pl-ent">requirement</span>></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"> <<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>1.6<span class="pl-pds">"</span></span>>samtools</<span class="pl-ent">requirement</span>></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"> <<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>2.2.1<span class="pl-pds">"</span></span>>cufflinks</<span class="pl-ent">requirement</span>></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"> <<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>2.7.1<span class="pl-pds">"</span></span>>blast</<span class="pl-ent">requirement</span>></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"> <<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>6.6.0.0<span class="pl-pds">"</span></span>>EMBOSS</<span class="pl-ent">requirement</span>></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"> <<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>0.8.0<span class="pl-pds">"</span></span>>seaborn</<span class="pl-ent">requirement</span>></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"> </<span class="pl-ent">requirements</span>></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"> <<span class="pl-ent">command</span> <span class="pl-e">interpreter</span>=<span class="pl-s"><span class="pl-pds">"</span>python<span class="pl-pds">"</span></span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">"</span>exit_code<span class="pl-pds">"</span></span>></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 == "Trypanosoma congolense":</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 == "Genomic":</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 == "Contig available":</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"><!--</span> name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 <span class="pl-c">--></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"><!--</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">--></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"><!--</span> name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 <span class="pl-c">--></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 == "Transcriptomic":</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 == "Contig available":</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"><!--</span> name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 <span class="pl-c">--></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"><!--</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">--></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"> </<span class="pl-ent">command</span>></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"> <<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>xname<span class="pl-pds">"</span></span> size = <span class="pl-s"><span class="pl-pds">"</span>30<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>text<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Test<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Prefix Name<span class="pl-pds">"</span></span> /></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>TrypType<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>species<span class="pl-pds">"</span></span> type = <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>Select Species<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Trypanosoma congolense<span class="pl-pds">"</span></span> <span class="pl-e">selected</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Trypanosoma vivax<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Trypanosoma congolense<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>analysis<span class="pl-pds">"</span></span> type = <span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Genomic or Transcriptomic Analysis?<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span> selected = <span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>preassem<span class="pl-pds">"</span></span> type = <span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Contig file available?<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span> selected = <span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>kmers<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>65<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">"</span>31<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">"</span>99<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Specify kmers<span class="pl-pds">"</span></span>></<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>inslen<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>400<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> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">"</span>999<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Insert length<span class="pl-pds">"</span></span>></<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>covcut<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>5<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> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">"</span>999<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Coverage cut off<span class="pl-pds">"</span></span>></<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>forward<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Forward NGS Read File<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reverse<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Reverse NGS Read File<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>contig<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>fasta<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Contig file<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> </<span class="pl-ent">conditional</span>></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"> </<span class="pl-ent">when</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>strain<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> label = <span class="pl-s"><span class="pl-pds">"</span>Select Reference Strain<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>forward<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Forward NGS Read File<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reverse<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Reverse NGS Read File<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> </<span class="pl-ent">conditional</span>></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"> </<span class="pl-ent">when</span>></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"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>Trypanosoma vivax<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>analysis<span class="pl-pds">"</span></span> type = <span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Genomic or Transcriptomic Analysis?<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span> selected = <span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>preassem<span class="pl-pds">"</span></span> type = <span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Contig file available?<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span> selected = <span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> <<span class="pl-ent">option</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></<span class="pl-ent">option</span>></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"> </<span class="pl-ent">param</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>kmers<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>65<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">"</span>31<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">"</span>99<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Specify kmers<span class="pl-pds">"</span></span>></<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>inslen<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>400<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> <span class="pl-e">max</span>=<span class="pl-s"><span class="pl-pds">"</span>999<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Insert length<span class="pl-pds">"</span></span>></<span class="pl-ent">param</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>forward<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Forward NGS Read File<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reverse<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Reverse NGS Read File<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>contig<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>fasta<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Contig file<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> </<span class="pl-ent">conditional</span>></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"> </<span class="pl-ent">when</span>> </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"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>vtreference<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>fasta<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>Reference File<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>forward<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Forward NGS Read File<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reverse<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>fastq<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Reverse NGS Read File<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">when</span>></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"> </<span class="pl-ent">conditional</span>></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"> </<span class="pl-ent">when</span>> </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"> </<span class="pl-ent">conditional</span>></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>P<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>PDF_Yes<span class="pl-pds">'</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">'</span>PDF_No<span class="pl-pds">'</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Export PDF of figures<span class="pl-pds">"</span></span> /></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"> </<span class="pl-ent">inputs</span>></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"> <<span class="pl-ent">outputs</span>></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"> <<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> name = <span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> label = <span class="pl-s"><span class="pl-pds">"</span>${xname.value}_html<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">outputs</span>></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"> <<span class="pl-ent">tests</span>></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"> <<span class="pl-ent">test</span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>xname<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Test<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>TrypType<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>species<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Trypanosoma congolense<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">conditional</span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>analysis<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">conditional</span>></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"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>preassem<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>/></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"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>contig<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>Test.fa<span class="pl-pds">"</span></span>/></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"> </<span class="pl-ent">conditional</span>></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"> <<span class="pl-ent">param</span> name = <span class="pl-s"><span class="pl-pds">"</span>P<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">'</span>PDF_No<span class="pl-pds">'</span></span>/></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"> <<span class="pl-ent">output</span> name = <span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> file = <span class="pl-s"><span class="pl-pds">'</span>Test_html<span class="pl-pds">'</span></span> ftype = <span class="pl-s"><span class="pl-pds">'</span>html<span class="pl-pds">'</span></span>/></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"> </<span class="pl-ent">test</span>></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"> </<span class="pl-ent">tests</span>></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"></<span class="pl-ent">tool</span>></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> | |
1299 </summary> | |
1300 <details-menu> | |
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> | |
1303 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li> | |
1304 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/VAP.xml">View git blame</a></li> | |
1305 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li> | |
1306 </ul> | |
1307 </details-menu> | |
1308 </details> | |
1309 | |
1310 </div> | |
1311 | |
1312 </div> | |
1313 | |
1314 | |
1315 | |
1316 <details class="details-reset details-overlay details-overlay-dark"> | |
1317 <summary data-hotkey="l" aria-label="Jump to line"></summary> | |
1318 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line"> | |
1319 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> | |
1320 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> | |
1321 <button type="submit" class="btn" data-close-dialog>Go</button> | |
1322 </form> </details-dialog> | |
1323 </details> | |
1324 | |
1325 | |
1326 | |
1327 </div> | |
1328 <div class="modal-backdrop js-touch-events"></div> | |
1329 </div> | |
1330 | |
1331 </main> | |
1332 </div> | |
1333 | |
1334 | |
1335 </div> | |
1336 | |
1337 | |
1338 <div class="footer container-lg width-full p-responsive" role="contentinfo"> | |
1339 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light "> | |
1340 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> | |
1341 <li class="mr-3 mr-lg-0">© 2019 <span title="1.77313s from unicorn-7478f9985c-h7jrf">GitHub</span>, Inc.</li> | |
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1349 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com"> | |
1350 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> | |
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1352 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> | |
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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> | |
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1374 You can’t perform that action at this time. | |
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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> | |
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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> | |
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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 |