Mercurial > repos > johnheap > vapper
changeset 14:7d1f86b4718d draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 15:56:10 -0400 |
| parents | 8c210b4ad003 |
| children | 597fe882966e |
| files | VAP.xml |
| diffstat | 1 files changed, 135 insertions(+), 1405 deletions(-) [+] |
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- <div class="BtnGroup"> - <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/VAP.xml">Raw</a> - <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> - <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/VAP.xml">History</a> - </div> +<tool id="VAP" name="VAPPER" version="1.1.0"> + <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> - <div> + <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.GT.analysis == "Transcriptomic": + Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path + #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 + #end if - 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<div itemprop="text" class="Box-body p-0 blob-wrapper data type-xml "> - -<table class="highlight tab-size js-file-line-container" data-tab-size="8"> - <tr> - <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> - <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> - </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> + <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 = "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="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 = "vtreference" type="data" format="fasta" label = "Reference File"/> + <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> + </conditional> - <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> - <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px"> - <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> - <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> - <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> - <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li> - </ul> - </details-menu> - </details> - - </div> - - </div> - - - - <details class="details-reset details-overlay details-overlay-dark"> - <summary data-hotkey="l" aria-label="Jump to line"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line"> - <!-- '"` --><!-- </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="✓" /> - <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> - <button type="submit" class="btn" data-close-dialog>Go</button> -</form> </details-dialog> - </details> - - - - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> - - </main> - </div> - - - </div> - - -<div class="footer container-lg width-full p-responsive" role="contentinfo"> - <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 "> - <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"> - <li class="mr-3 mr-lg-0">© 2019 <span title="1.77313s from unicorn-7478f9985c-h7jrf">GitHub</span>, Inc.</li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li> - <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li> - </ul> + <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> + </inputs> - <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com"> - <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> -</a> - <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"> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li> - <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li> - - </ul> - </div> - <div class="d-flex flex-justify-center pb-6"> - <span class="f6 text-gray-light"></span> - </div> -</div> - - - - <div id="ajax-error-message" class="ajax-error-message flash flash-error"> - <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> - <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> - <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> - </button> - You can’t perform that action at this time. - </div> - + <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> - <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script> - <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script> - - <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script> - - - - <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden - > - <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> - <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <template id="site-details-dialog"> - <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open> - <summary role="button" aria-label="Close dialog"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> - <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> - <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> - </button> - <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> - </details-dialog> - </details> -</template> - - <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0"> - <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;"> - </div> -</div> - - <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div> - - </body> -</html> -