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VAP.xml |
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| diff -r a0d5e1f5bec0 -r 6450a72e8f6b VAP.xml --- a/VAP.xml Mon Jun 03 14:09:49 2019 -0400 +++ b/VAP.xml Mon Jun 03 14:11:12 2019 -0400 |
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| b'@@ -1,125 +1,1412 @@\n-<tool id="VAP" name="VAPPER" version="1.0.0">\r\n- <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description>\r\n-\t<requirements>\r\n- <requirement type="package" version="1.2.10">velvet</requirement>\r\n- <requirement type="package" version="3.1b2">HMMER</requirement>\r\n- <requirement type="package" version="2.2.6">bowtie2</requirement>\r\n- <requirement type="package" version="1.6">samtools</requirement>\r\n- <requirement type="package" version="2.2.1">cufflinks</requirement>\r\n- <requirement type="package" version="2.7.1">blast</requirement>\r\n-\t\t<requirement type="package" version="6.6.0.0">EMBOSS</requirement>\r\n-\t\t<requirement type="package" version="0.8.0">seaborn</requirement>\r\n-\t</requirements>\r\n-\r\n-\r\n- <command interpreter="python" detect_errors="exit_code">\r\n- #if $TrypType.species == "Trypanosoma congolense":\r\n- #if $TrypType.GT.analysis == "Genomic":\r\n- #if $TrypType.GT.contigs.preassem == "Contig available":\r\n- <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->\r\n- Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path\r\n- #else\r\n- <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->\r\n- 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\r\n- #end if\r\n- #else\r\n- <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 -->\r\n- Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path\r\n- #end if\r\n- #else\r\n- #if $TrypType.contigs.preassem == "Contig available":\r\n- <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->\r\n- Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path\r\n- #else\r\n- <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->\r\n- 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\r\n- #end if\r\n- #end if\r\n-\r\n- </command>\r\n-\r\n- <inputs>\r\n- <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" />\r\n- <conditional name = "TrypType">\r\n- <param name = "species" type = \'select\' label="Select Species">\r\n- <option value = "Trypanosoma congolense" selected="true"></option>\r\n- <option value = "Trypanosoma vivax"></option>\r\n- </param>\r\n- <when value = "Trypanosoma congolense">\r\n- <conditional name = "GT">\r\n- <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">\r\n- <option value = "Genomic" selected = "true"></option>\r\n- <option value = "Transcriptomic"></option>\r\n- </param>\r\n- <when value = "Genomic">\r\n- <conditional name = "contigs">\r\n- <param name = "preassem" type = "select" label = "Contig file available?">\r\n- <option value = "Full assembly" selected = "true"></option>\r\n- <option value = "Contig available"></option>\r\n- </param>\r\n- '..b'a-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>\n+\n+ </ul>\n+ </div>\n+ <div class="d-flex flex-justify-center pb-6">\n+ <span class="f6 text-gray-light"></span>\n+ </div>\n+</div>\n+\n+\n+\n+ <div id="ajax-error-message" class="ajax-error-message flash flash-error">\n+ <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 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11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>\n+ <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>\n+ <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>\n+ </div>\n+ <template id="site-details-dialog">\n+ <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>\n+ <summary role="button" aria-label="Close dialog"></summary>\n+ <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">\n+ <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>\n+ <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 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