Mercurial > repos > elixir-it > mutect2
view mutect2_macros_add_loc.xml @ 1:fbfc333f3eec draft
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| author | elixir-it |
|---|---|
| date | Thu, 28 Jun 2018 06:07:29 -0400 |
| parents | |
| children | 1f25d6323970 |
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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> </button> <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" aria-label="You must be signed in to make or propose changes"> <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> </button> </div> <div class="file-info"> 23 lines (22 sloc) <span class="file-info-divider"></span> 1.39 KB </div> </div> <div itemprop="text" class="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">macros</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">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> </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">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> </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">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> </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">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> </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">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> </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">param</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">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> </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">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> </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">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> </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">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> </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">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> </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"> </<span class="pl-ent">options</span>></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"> <<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> </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">param</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"> </<span class="pl-ent">when</span>></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"> <<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> </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"> <<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> </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-ent">when</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"> </<span 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