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comparison mutect2_macros_add_loc.xml @ 1:fbfc333f3eec draft

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author elixir-it
date Thu, 28 Jun 2018 06:07:29 -0400
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children 1f25d6323970
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558
559
560
561 <div itemprop="text" class="blob-wrapper data type-xml">
562 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
563 <tr>
564 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
565 <td id="LC1" class="blob-code blob-code-inner js-file-line">&lt;<span class="pl-ent">macros</span>&gt;</td>
566 </tr>
567 <tr>
568 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
569 <td id="LC2" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">macro</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reference_loc<span class="pl-pds">&quot;</span></span>&gt;</td>
570 </tr>
571 <tr>
572 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
573 <td id="LC3" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">conditional</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reference_source<span class="pl-pds">&quot;</span></span>&gt;</td>
574 </tr>
575 <tr>
576 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
577 <td id="LC4" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>reference_source_selector<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Will you select a reference genome from your history or use a built-in index?<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Built-ins were indexed using default options. See `Indexes` section of help below<span class="pl-pds">&quot;</span></span>&gt;</td>
578 </tr>
579 <tr>
580 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
581 <td id="LC5" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cached<span class="pl-pds">&quot;</span></span>&gt;Use a built-in genome index&lt;/<span class="pl-ent">option</span>&gt;</td>
582 </tr>
583 <tr>
584 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
585 <td id="LC6" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>history<span class="pl-pds">&quot;</span></span>&gt;Use a genome from history and build index&lt;/<span class="pl-ent">option</span>&gt;</td>
586 </tr>
587 <tr>
588 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
589 <td id="LC7" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
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591 <tr>
592 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
593 <td id="LC8" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>cached<span class="pl-pds">&quot;</span></span>&gt;</td>
594 </tr>
595 <tr>
596 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
597 <td id="LC9" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>ref_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>select<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Using reference genome<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Select genome from the list<span class="pl-pds">&quot;</span></span>&gt;</td>
598 </tr>
599 <tr>
600 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
601 <td id="LC10" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">options</span> <span class="pl-e">from_data_table</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>mutect2_indexes<span class="pl-pds">&quot;</span></span>&gt;</td>
602 </tr>
603 <tr>
604 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
605 <td id="LC11" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">filter</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>sort_by<span class="pl-pds">&quot;</span></span> <span class="pl-e">column</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>2<span class="pl-pds">&quot;</span></span> /&gt;</td>
606 </tr>
607 <tr>
608 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
609 <td id="LC12" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>no_options<span class="pl-pds">&quot;</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>No indexes are available<span class="pl-pds">&quot;</span></span> /&gt;</td>
610 </tr>
611 <tr>
612 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
613 <td id="LC13" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">options</span>&gt;</td>
614 </tr>
615 <tr>
616 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
617 <td id="LC14" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>no_options<span class="pl-pds">&quot;</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>A built-in reference genome is not available for the build associated with the selected input file<span class="pl-pds">&quot;</span></span>/&gt;</td>
618 </tr>
619 <tr>
620 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
621 <td id="LC15" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">param</span>&gt;</td>
622 </tr>
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625 <td id="LC16" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt;</td>
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627 <tr>
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630 </tr>
631 <tr>
632 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
633 <td id="LC18" class="blob-code blob-code-inner js-file-line"> &lt;<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>ref_file<span class="pl-pds">&quot;</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>data<span class="pl-pds">&quot;</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>fasta<span class="pl-pds">&quot;</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>Use the following dataset as the reference sequence<span class="pl-pds">&quot;</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">&quot;</span>You can upload a FASTA sequence to the history and use it as reference<span class="pl-pds">&quot;</span></span> /&gt;</td>
634 </tr>
635 <tr>
636 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
637 <td id="LC19" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">when</span>&gt; </td>
638 </tr>
639 <tr>
640 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
641 <td id="LC20" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">conditional</span>&gt;</td>
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643 <tr>
644 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
645 <td id="LC21" class="blob-code blob-code-inner js-file-line"> &lt;/<span class="pl-ent">macro</span>&gt;</td>
646 </tr>
647 <tr>
648 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
649 <td id="LC22" class="blob-code blob-code-inner js-file-line">&lt;/<span class="pl-ent">macros</span>&gt;</td>
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