Mercurial > repos > johnheap > vapper
changeset 10:6450a72e8f6b draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 14:11:12 -0400 |
| parents | a0d5e1f5bec0 |
| children | c4463e84a7ea |
| files | VAP.xml |
| diffstat | 1 files changed, 1412 insertions(+), 125 deletions(-) [+] |
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--- a/VAP.xml Mon Jun 03 14:09:49 2019 -0400 +++ b/VAP.xml Mon Jun 03 14:11:12 2019 -0400 @@ -1,125 +1,1412 @@ -<tool id="VAP" name="VAPPER" version="1.0.0"> - <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description> - <requirements> - <requirement type="package" version="1.2.10">velvet</requirement> - <requirement type="package" version="3.1b2">HMMER</requirement> - <requirement type="package" version="2.2.6">bowtie2</requirement> - <requirement type="package" version="1.6">samtools</requirement> - <requirement type="package" version="2.2.1">cufflinks</requirement> - <requirement type="package" version="2.7.1">blast</requirement> - <requirement type="package" version="6.6.0.0">EMBOSS</requirement> - <requirement type="package" version="0.8.0">seaborn</requirement> - </requirements> - - - <command interpreter="python" detect_errors="exit_code"> - #if $TrypType.species == "Trypanosoma congolense": - #if $TrypType.GT.analysis == "Genomic": - #if $TrypType.GT.contigs.preassem == "Contig available": - <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> - Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path - #else - <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> - 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 - #end if - #else - <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 --> - Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path - #end if - #else - #if $TrypType.contigs.preassem == "Contig available": - <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> - Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path - #else - <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> - 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 - #end if - #end if - - </command> - - <inputs> - <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" /> - <conditional name = "TrypType"> - <param name = "species" type = 'select' label="Select Species"> - <option value = "Trypanosoma congolense" selected="true"></option> - <option value = "Trypanosoma vivax"></option> - </param> - <when value = "Trypanosoma congolense"> - <conditional name = "GT"> - <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> - <option value = "Genomic" selected = "true"></option> - <option value = "Transcriptomic"></option> - </param> - <when value = "Genomic"> - <conditional name = "contigs"> - <param name = "preassem" type = "select" label = "Contig file available?"> - <option value = "Full assembly" selected = "true"></option> - <option value = "Contig available"></option> - </param> - <when value = "Full assembly"> - <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> - <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> - <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param> - <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> - <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> - </when> - <when value = "Contig available"> - <param name="contig" type="data" format="fasta" label="Contig file"/> - </when> - </conditional> - </when> - <when value = "Transcriptomic"> - <param name = "strain" type="select" label = "Select Reference Strain"> - <option value = "Tc148"></option> - <option value = "IL3000"></option> - </param> - <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> - <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> - </when> - </conditional> - </when> - <when value="Trypanosoma vivax"> - <conditional name = "contigs"> - <param name = "preassem" type = "select" label = "Contig file available?"> - <option value = "Full assembly" selected = "true"></option> - <option value = "Contig available"></option> - </param> - <when value = "Full assembly"> - <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> - <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> - <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> - <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> - </when> - <when value = "Contig available"> - <param name="contig" type="data" format="fasta" label="Contig file"/> - </when> - </conditional> - </when> - </conditional> - - <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> - </inputs> - - <outputs> - <data format="html" name = "html_file" label = "${xname.value}_html"/> - </outputs> - <tests> - <test> - <param name = "xname" value = "Test"/> - <conditional name = "TrypType"> - <param name = "species" value = "Trypanosoma congolense"/> - </conditional> - <conditional name = "GT"> - <param name = "analysis" value = "Genomic"/> - </conditional> - <conditional name = "contigs"> - <param name = "preassem" value = "Contig available"/> - <param name="contig" value = "Test.fa"/> - </conditional> - <param name = "P" value = 'PDF_No'/> - <output name = "html_file" file = 'Test_html' ftype = 'html'/> - </test> - </tests> -</tool> - 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+ <details class="HeaderMenu-details details-overlay details-reset width-full"> + <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> + Explore + <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"> + <path d="M1,1l6.2,6L13,1"></path> + </svg> + </summary> + + <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"> + <ul class="list-style-none mb-3"> + <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> + </ul> + + <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> + <ul class="list-style-none mb-3"> + <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> + <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> + <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> + <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> + <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> + </ul> + + <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> + <ul class="list-style-none mb-0"> + <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> + <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> + <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> + </ul> + </div> + </details> + </li> + + <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> + <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> + </li> + + <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 "> + <details class="HeaderMenu-details details-overlay details-reset width-full"> + <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> + Pricing + <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"> + <path d="M1,1l6.2,6L13,1"></path> + </svg> + </summary> + + <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"> + <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> + + <ul class="list-style-none mb-3"> + <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> + <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> + </ul> + + <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> + <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> + <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> + </ul> + </div> + </details> + </li> + </ul> + </nav> + + <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> + <div class="d-lg-flex mb-3 mb-lg-0"> + <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" + role="combobox" + aria-owns="jump-to-results" + aria-label="Search or jump to" + aria-haspopup="listbox" + aria-expanded="false" +> + <div class="position-relative"> + <!-- '"` --><!-- </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="✓" /> + <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"> + <input type="text" + 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" + data-hotkey="s,/" + name="q" + value="" + placeholder="Search" + data-unscoped-placeholder="Search GitHub" + data-scoped-placeholder="Search" + autocapitalize="off" + aria-autocomplete="list" + aria-controls="jump-to-results" + aria-label="Search" + data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=KTCloZOsmcJnQG8+9Rpx1bhv3g0Y6RphAwXNxB0AQyG1y/I19pdeBJolo4nekuHBWhvAt65+3d/8rLCh6xmeUw==" + spellcheck="false" + autocomplete="off" + > + <input type="hidden" class="js-site-search-type-field" name="type" > + <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> + + <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> + +<ul class="d-none js-jump-to-suggestions-template-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> + <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=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <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> + <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> + <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> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <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"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + +</ul> + +<ul class="d-none js-jump-to-no-results-template-container"> + <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> + <span class="text-gray">No suggested jump to results</span> + </li> +</ul> + +<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"> + + +<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"> + <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=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <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> + <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> + <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> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <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"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + + +<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"> + <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=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <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> + <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> + <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> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <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"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + +</ul> + + </div> + </label> +</form> </div> +</div> + + </div> + + <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"99EF:3DF4:A496E:120BBA:5CF562BE","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/VAP.xml","referrer":null,"user_id":null}}" data-hydro-click-hmac="4f690ef143e2ef8459c43b1cbf0fd9a9eec10f2a80477c079b3de11e63ff5f09" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FVAP.xml"> + Sign in +</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99EF:3DF4:A496E:120BBA:5CF562BE","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/VAP.xml","referrer":null,"user_id":null}}" data-hydro-click-hmac="ec8ff730fd1d25dbc45baf1260ca99d2d34f31dc8b2a02c77ee87f2053979769" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> + Sign up +</a> </div> + </div> + </div> +</header> + + </div> + + <div id="start-of-content" class="show-on-focus"></div> + + + <div id="js-flash-container"> + +</div> + + + + <div class="application-main " data-commit-hovercards-enabled> + <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> + <main > + + + + + + + + + + + <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 "> + <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block"> + + <ul 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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> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">description</span>>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> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirements</span>></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>package<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>1.6<span class="pl-pds">"</span></span>>samtools</<span class="pl-ent">requirement</span>></td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">requirements</span>></td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"> #if $TrypType.species == "Trypanosoma congolense":</td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.analysis == "Genomic":</td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.contigs.preassem == "Contig available":</td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"> <span class="pl-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> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line"> Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path</td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line"> #else</td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"> <span class="pl-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> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code blob-code-inner js-file-line"> 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> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code blob-code-inner js-file-line"> #end if</td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code blob-code-inner js-file-line"> #else</td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code blob-code-inner js-file-line"> <span class="pl-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> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code blob-code-inner js-file-line"> Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path</td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code blob-code-inner js-file-line"> #end if</td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code blob-code-inner js-file-line"> #else</td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code blob-code-inner js-file-line"> #if $TrypType.GT.analysis == "Transcriptomic":</td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code blob-code-inner js-file-line"> Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path</td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code blob-code-inner js-file-line"> #else</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code blob-code-inner js-file-line"> #if $TrypType.contigs.preassem == "Contig available":</td> + </tr> + <tr> + <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> + <td id="LC34" class="blob-code blob-code-inner js-file-line"> <span class="pl-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> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code blob-code-inner js-file-line"> Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path</td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code blob-code-inner js-file-line"> #else</td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code blob-code-inner js-file-line"> <span class="pl-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> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code blob-code-inner js-file-line"> 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> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code blob-code-inner js-file-line"> #end if</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code blob-code-inner js-file-line"> #end if </td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code blob-code-inner js-file-line"> #end if</td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">command</span>></td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">inputs</span>></td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>TrypType<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> + <td id="LC48" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> + <td id="LC49" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> + <td id="LC50" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> + <td id="LC51" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> + <td id="LC52" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Trypanosoma congolense<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> + <td id="LC53" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> + <td id="LC54" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> + <td id="LC55" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> + <td id="LC56" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> + <td id="LC57" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> + <td id="LC58" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> + <td id="LC59" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> + <td id="LC60" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> + <td id="LC61" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> + <td id="LC62" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> + <td id="LC63" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> + <td id="LC64" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> + <td id="LC65" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> + <td id="LC66" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> + <td id="LC67" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> + <td id="LC68" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> + <td id="LC69" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> + <td id="LC70" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> + <td id="LC71" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> + <td id="LC72" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> + <td id="LC73" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> + <td id="LC74" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> + <td id="LC75" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> + <td id="LC76" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> + <td id="LC77" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> + <td id="LC78" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> + <td id="LC79" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> + <td id="LC80" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> + <td id="LC81" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> + <td id="LC82" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> + <td id="LC83" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> + <td id="LC84" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> + <td id="LC85" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> + <td id="LC86" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> + <td id="LC87" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> + <td id="LC88" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> + <td id="LC89" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> + <td id="LC90" class="blob-code blob-code-inner js-file-line"> <<span class="pl-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> + </tr> + <tr> + <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> + <td id="LC91" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> + <td id="LC92" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Genomic<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> + <td id="LC93" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> + <td id="LC94" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> + <td id="LC95" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> 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> + </tr> + <tr> + <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> + <td id="LC96" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> 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> + </tr> + <tr> + <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> + <td id="LC97" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> + <td id="LC98" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Full assembly<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> + <td id="LC99" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> + <td id="LC100" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> + <td id="LC101" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> + <td id="LC102" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> + <td id="LC103" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> + <td id="LC104" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Contig available<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> + <td id="LC105" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> + <td id="LC106" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> + <td id="LC107" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> + <td id="LC108" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>> </td> + </tr> + <tr> + <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> + <td id="LC109" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> value = <span class="pl-s"><span class="pl-pds">"</span>Transcriptomic<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> + <td id="LC110" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> + <td id="LC111" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> + <td id="LC112" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> + <td id="LC113" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> + <td id="LC114" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> + <td id="LC115" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>> </td> + </tr> + <tr> + <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> + <td id="LC116" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> + <td id="LC117" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> + <td id="LC118" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> + <td id="LC119" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">inputs</span>></td> + </tr> + <tr> + <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> + <td id="LC120" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> + <td id="LC121" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">outputs</span>></td> + </tr> + <tr> + <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> + <td id="LC122" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> + <td id="LC123" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">outputs</span>></td> + </tr> + <tr> + <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> + <td id="LC124" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">tests</span>></td> + </tr> + <tr> + <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> + <td id="LC125" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td> + </tr> + <tr> + <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> + <td id="LC126" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> + <td id="LC127" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>TrypType<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> + <td id="LC128" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> + <td id="LC129" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> + <td id="LC130" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>GT<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> + <td id="LC131" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> + <td id="LC132" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> + <td id="LC133" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> name = <span class="pl-s"><span class="pl-pds">"</span>contigs<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> + <td id="LC134" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> + <td id="LC135" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> + <td id="LC136" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> + <td id="LC137" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> 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> + </tr> + <tr> + <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> + <td id="LC138" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">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> + </tr> + <tr> + <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> + <td id="LC139" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td> + </tr> + <tr> + <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> + <td id="LC140" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">tests</span>></td> + </tr> + <tr> + <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> + <td id="LC141" class="blob-code blob-code-inner js-file-line"></<span class="pl-ent">tool</span>></td> + </tr> + <tr> + <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> + <td id="LC142" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> +</table> + + <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> + <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> + <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> + </summary> + <details-menu> 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