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485 </a>
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487 Copy path
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488 </clipboard-copy>
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489 </div>
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491 <span class="repo-root js-repo-root"><span class="js-path-segment"><a data-pjax="true" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper"><span>GDC-DNA-Seq-pipeline-galaxy-wrapper</span></a></span></span><span class="separator">/</span><span class="js-path-segment"><a data-pjax="true" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper"><span>Mutect2-wrapper</span></a></span><span class="separator">/</span><strong class="final-path">mutect2_macros_add_loc.xml</strong>
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499 <a class="commit-tease-sha" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/163a49b5746b79e0245049afc0fcfb8ca220e494" data-pjax>
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500 163a49b
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501 </a>
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502 <relative-time datetime="2018-06-27T09:23:15Z">Jun 27, 2018</relative-time>
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503 </span>
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504 <div>
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505 <a rel="author" data-skip-pjax="true" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli"><img class="avatar" src="https://avatars0.githubusercontent.com/u/33326058?s=40&v=4" width="20" height="20" alt="@pmandreoli" /></a>
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506 <a class="user-mention" rel="author" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli">pmandreoli</a>
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507 <a data-pjax="true" title="change" class="message" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/163a49b5746b79e0245049afc0fcfb8ca220e494">change</a>
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508 </div>
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509
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510 <div class="commit-tease-contributors">
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511 <button type="button" class="btn-link muted-link contributors-toggle" data-facebox="#blob_contributors_box">
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512 <strong>1</strong>
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516 </div>
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518 <div id="blob_contributors_box" style="display:none">
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519 <h2 class="facebox-header" data-facebox-id="facebox-header">Users who have contributed to this file</h2>
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520 <ul class="facebox-user-list" data-facebox-id="facebox-description">
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521 <li class="facebox-user-list-item">
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522 <a class="d-inline-block" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli"><img src="https://avatars1.githubusercontent.com/u/33326058?s=48&v=4" width="24" height="24" alt="@pmandreoli" /></a>
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523 <a data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli">pmandreoli</a>
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524 </li>
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536 <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/raw/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">Raw</a>
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537 <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blame/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">Blame</a>
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538 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">History</a>
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539 </div>
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540
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541
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542 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw"
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543 aria-label="You must be signed in to make or propose changes">
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544 <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
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545 </button>
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546 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
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547 aria-label="You must be signed in to make or propose changes">
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548 <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg>
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553 23 lines (22 sloc)
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555 1.39 KB
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556 </div>
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557 </div>
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560
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561 <div itemprop="text" class="blob-wrapper data type-xml">
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562 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
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563 <tr>
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564 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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565 <td id="LC1" class="blob-code blob-code-inner js-file-line"><<span class="pl-ent">macros</span>></td>
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566 </tr>
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567 <tr>
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568 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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569 <td id="LC2" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">macro</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reference_loc<span class="pl-pds">"</span></span>></td>
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570 </tr>
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571 <tr>
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572 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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573 <td id="LC3" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reference_source<span class="pl-pds">"</span></span>></td>
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574 </tr>
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575 <tr>
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576 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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577 <td id="LC4" 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>reference_source_selector<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> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Will you select a reference genome from your history or use a built-in index?<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Built-ins were indexed using default options. See `Indexes` section of help below<span class="pl-pds">"</span></span>></td>
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578 </tr>
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579 <tr>
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580 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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581 <td id="LC5" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cached<span class="pl-pds">"</span></span>>Use a built-in genome index</<span class="pl-ent">option</span>></td>
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582 </tr>
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583 <tr>
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584 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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585 <td id="LC6" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>history<span class="pl-pds">"</span></span>>Use a genome from history and build index</<span class="pl-ent">option</span>></td>
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586 </tr>
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587 <tr>
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588 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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589 <td id="LC7" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td>
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590 </tr>
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591 <tr>
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592 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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593 <td id="LC8" 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>cached<span class="pl-pds">"</span></span>></td>
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594 </tr>
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595 <tr>
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596 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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597 <td id="LC9" 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>ref_file<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> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Using reference genome<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Select genome from the list<span class="pl-pds">"</span></span>></td>
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598 </tr>
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599 <tr>
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600 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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601 <td id="LC10" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">options</span> <span class="pl-e">from_data_table</span>=<span class="pl-s"><span class="pl-pds">"</span>mutect2_indexes<span class="pl-pds">"</span></span>></td>
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602 </tr>
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603 <tr>
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604 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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605 <td id="LC11" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">filter</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>sort_by<span class="pl-pds">"</span></span> <span class="pl-e">column</span>=<span class="pl-s"><span class="pl-pds">"</span>2<span class="pl-pds">"</span></span> /></td>
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606 </tr>
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609 <td id="LC12" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>no_options<span class="pl-pds">"</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">"</span>No indexes are available<span class="pl-pds">"</span></span> /></td>
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610 </tr>
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612 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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613 <td id="LC13" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">options</span>></td>
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614 </tr>
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615 <tr>
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616 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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617 <td id="LC14" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>no_options<span class="pl-pds">"</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">"</span>A built-in reference genome is not available for the build associated with the selected input file<span class="pl-pds">"</span></span>/></td>
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618 </tr>
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619 <tr>
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621 <td id="LC15" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td>
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622 </tr>
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625 <td id="LC16" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td>
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626 </tr>
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627 <tr>
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629 <td id="LC17" 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>history<span class="pl-pds">"</span></span>></td>
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630 </tr>
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631 <tr>
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632 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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633 <td id="LC18" 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>ref_file<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>Use the following dataset as the reference sequence<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>You can upload a FASTA sequence to the history and use it as reference<span class="pl-pds">"</span></span> /></td>
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634 </tr>
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635 <tr>
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636 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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637 <td id="LC19" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>> </td>
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638 </tr>
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639 <tr>
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640 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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641 <td id="LC20" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td>
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642 </tr>
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645 <td id="LC21" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">macro</span>></td>
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646 </tr>
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647 <tr>
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648 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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649 <td id="LC22" class="blob-code blob-code-inner js-file-line"></<span class="pl-ent">macros</span>></td>
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650 </tr>
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651 </table>
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653 <div class="BlobToolbar position-absolute js-file-line-actions dropdown js-menu-container js-select-menu d-none" aria-hidden="true">
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655 <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>
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656 </button>
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657 <div class="dropdown-menu-content js-menu-content" id="inline-file-actions">
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658 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2">
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659 <li><clipboard-copy class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
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660 <li><clipboard-copy class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
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661 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blame/bf2daac4de1923ee01fd86ad0683e1ef5a9bd82e/Mutect2-wrapper/mutect2_macros_add_loc.xml">View git blame</a></li>
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662 <li><a class="dropdown-item" id="js-new-issue" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/issues/new">Open new issue</a></li>
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663 </ul>
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664 </div>
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671 <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button>
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672 <div id="jump-to-line" style="display:none">
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673 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" />
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674 <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
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675 <button type="submit" class="btn">Go</button>
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676 </form> </div>
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677
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679 </div>
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