Mercurial > repos > eduardo > download_and_align
view url2bowtie/tool-data/test-data2 @ 7:8accf8976cf7
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| author | eduardo |
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| date | Mon, 03 Aug 2015 05:36:36 -0400 |
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value="oHnhBUKtIFc/i+gj1F8SdSSK6r2vwLo0csLvt6huBR6W4GyuyAl915tvYyDR2eLrs8hxzyu3b0Ooq8FsVZjYww==" /></div> <button class="btn-link tooltipped tooltipped-e" type="submit" data-disable-with="working…" aria-label="Fork this project and create a new file"> <span class="js-new-blob-submit octicon octicon-plus"></span> </button> </form> </div> </div> <div class="commit commit-tease js-details-container" > <p class="commit-title "> <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling. The reusable macro file has: - Defines widgets for common read group parameters. - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers). - The conditional (used by mappers) has fours modes: - Set according the specification (only ID required - has all parameters). Current BWA approach. - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``. - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?) - Do not set read groups. - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - An example "mapper" test tool which demonstrates optionally including read groups. - An example read group assign test tool which demonstrates unconditionally specifying macros. In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs. This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool. Updates from original version: - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). Smaller Notes: The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: ``` -@RG ID:rg1 SM: PL:CAPILLARY -@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat +@RG ID:rg1 PL:CAPILLARY +@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat ```">Unify and collectionify read group handling.</a> <span class="hidden-text-expander inline"><a href="#" class="js-details-target">…</a></span> </p> <div class="commit-desc"><pre>The reusable macro file has: - Defines widgets for common read group parameters. - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers). - The conditional (used by mappers) has fours modes: - Set according the specification (only ID required - has all parameters). Current BWA approach. - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``. - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?) - Do not set read groups. - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - An example "mapper" test tool which demonstrates optionally including read groups. - An example read group assign test tool which demonstrates unconditionally specifying macros. In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs. This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool. Updates from original version: - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). Smaller Notes: The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: ``` -<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY -<a href="https://github.com/PG" class="user-mention">@PG</a> ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r <a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat +<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY +<a href="https://github.com/PG" class="user-mention">@PG</a> ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r <a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat ```</pre></div> <div class="commit-meta"> <button aria-label="Copy SHA" 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href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a> </span> </td> <td class="age"> <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span> </td> </tr> <tr> <td class="icon"> <span class="octicon octicon-file-text"></span> <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> </td> <td class="content"> <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-test2.bam" class="js-directory-link" id="fcef5de0c5311dd568ad01705dfbcf96-12df83659d247d24c2a6dbb51740559bc73643b9" title="bowtie2-test2.bam">bowtie2-test2.bam</a></span> </td> <td class="message"> <span class="css-truncate css-truncate-target"> <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling. The reusable macro file has: - Defines widgets for common read group parameters. - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers). - The conditional (used by mappers) has fours modes: - Set according the specification (only ID required - has all parameters). Current BWA approach. - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``. - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?) - Do not set read groups. - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - An example "mapper" test tool which demonstrates optionally including read groups. - An example read group assign test tool which demonstrates unconditionally specifying macros. In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs. This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool. Updates from original version: - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). Smaller Notes: The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: ``` -@RG ID:rg1 SM: PL:CAPILLARY -@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat +@RG ID:rg1 PL:CAPILLARY +@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat ```">Unify and collectionify read group handling.</a> </span> </td> <td class="age"> <span class="css-truncate css-truncate-target"><time datetime="2015-05-07T19:31:09Z" is="time-ago">May 7, 2015</time></span> </td> </tr> </tbody> </table> </div> </div> </div> <div class="modal-backdrop"></div> </div> </div> </div><!-- /.wrapper --> <div class="container"> <div class="site-footer" role="contentinfo"> <ul class="site-footer-links right"> <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li> </ul> <a href="https://github.com" aria-label="Homepage"> <span class="mega-octicon octicon-mark-github" title="GitHub"></span> </a> <ul class="site-footer-links"> <li>© 2015 <span title="0.06882s from github-fe127-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> </ul> </div> </div> <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> <div class="fullscreen-container js-suggester-container"> <div class="textarea-wrap"> <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder="" aria-label=""></textarea> <div class="suggester-container"> <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> </div> </div> </div> <div class="fullscreen-sidebar"> <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> <span class="mega-octicon octicon-screen-normal"></span> </a> <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" aria-label="Switch themes"> <span class="octicon octicon-color-mode"></span> </a> </div> </div> <div id="ajax-error-message" class="flash flash-error"> <span class="octicon octicon-alert"></span> <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> Something went wrong with that request. 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