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comparison massPix @ 0:dada1f17021d draft

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author metaboflow_cam
date Tue, 24 Sep 2019 04:37:32 -0400
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545 Dismiss
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565 <div class="overall-summary overall-summary-bottomless">
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568 <a data-pjax href="/wanchanglin/massPix/commits/master">
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570 <span class="num text-emphasized">
571 24
572 </span>
573 commits
574 </a>
575 </li>
576 <li>
577 <a data-pjax href="/wanchanglin/massPix/branches">
578 <svg class="octicon octicon-git-branch" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 5c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v.3c-.02.52-.23.98-.63 1.38-.4.4-.86.61-1.38.63-.83.02-1.48.16-2 .45V4.72a1.993 1.993 0 0 0-1-3.72C.88 1 0 1.89 0 3a2 2 0 0 0 1 1.72v6.56c-.59.35-1 .99-1 1.72 0 1.11.89 2 2 2 1.11 0 2-.89 2-2 0-.53-.2-1-.53-1.36.09-.06.48-.41.59-.47.25-.11.56-.17.94-.17 1.05-.05 1.95-.45 2.75-1.25S8.95 7.77 9 6.73h-.02C9.59 6.37 10 5.73 10 5zM2 1.8c.66 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2C1.35 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2zm0 12.41c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm6-8c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
579 <span class="num text-emphasized">
580 1
581 </span>
582 branch
583 </a>
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588 <a href="/wanchanglin/massPix/releases">
589 <svg class="octicon octicon-tag" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.73 1.73C7.26 1.26 6.62 1 5.96 1H3.5C2.13 1 1 2.13 1 3.5v2.47c0 .66.27 1.3.73 1.77l6.06 6.06c.39.39 1.02.39 1.41 0l4.59-4.59a.996.996 0 0 0 0-1.41L7.73 1.73zM2.38 7.09c-.31-.3-.47-.7-.47-1.13V3.5c0-.88.72-1.59 1.59-1.59h2.47c.42 0 .83.16 1.13.47l6.14 6.13-4.73 4.73-6.13-6.15zM3.01 3h2v2H3V3h.01z"/></svg>
590 <span class="num text-emphasized">
591 0
592 </span>
593 releases
594 </a>
595 </li>
596
597
598 <li >
599 <include-fragment src="/wanchanglin/massPix/contributors_size">
600 <a href="/wanchanglin/massPix/graphs/contributors">
601 <svg class="octicon octicon-organization" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 12.999c0 .439-.45 1-1 1H7.995c-.539 0-.994-.447-.995-.999H1c-.54 0-1-.561-1-1 0-2.634 3-4 3-4s.229-.409 0-1c-.841-.621-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.442.58 2.5 3c.058 2.41-.159 2.379-1 3-.229.59 0 1 0 1s1.549.711 2.42 2.088C9.196 9.369 10 8.999 10 8.999s.229-.409 0-1c-.841-.62-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.437.581 2.495 3c.059 2.41-.158 2.38-1 3-.229.59 0 1 0 1s3.005 1.366 3.005 4z"/></svg>
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612 <div class="d-flex repository-lang-stats-graph">
613 <span class="language-color" aria-label="R 96.7%" style="width:96.7%; background-color:#198CE7;" itemprop="keywords">R</span>
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615 <span class="language-color" aria-label="Batchfile 0.9%" style="width:0.9%; background-color:#C1F12E;" itemprop="keywords">Batchfile</span>
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619 <ol class="repository-lang-stats-numbers">
620 <li>
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622 <span class="color-block language-color" style="background-color:#198CE7;"></span>
623 <span class="lang">R</span>
624 <span class="percent">96.7%</span>
625 </a>
626 </li>
627 <li>
628 <a href="/wanchanglin/massPix/search?l=shell" data-ga-click="Repository, language stats search click, location:repo overview">
629 <span class="color-block language-color" style="background-color:#89e051;"></span>
630 <span class="lang">Shell</span>
631 <span class="percent">2.4%</span>
632 </a>
633 </li>
634 <li>
635 <a href="/wanchanglin/massPix/search?l=batchfile" data-ga-click="Repository, language stats search click, location:repo overview">
636 <span class="color-block language-color" style="background-color:#C1F12E;"></span>
637 <span class="lang">Batchfile</span>
638 <span class="percent">0.9%</span>
639 </a>
640 </li>
641 </ol>
642 </div>
643 </details>
644
645
646
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648
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653 <summary class="btn btn-sm select-menu-button css-truncate"
654 data-hotkey="w"
655 title="Switch branches or tags">
656 <i>Branch:</i>
657 <span class="css-truncate-target" data-menu-button>master</span>
658 </summary>
659
660 <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/wanchanglin/massPix/ref-list/master?source_action=disambiguate&amp;source_controller=files" preload>
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685 <summary class="btn btn-sm ml-2 btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;repository.click&quot;,&quot;payload&quot;:{&quot;repository_id&quot;:130720555,&quot;target&quot;:&quot;CLONE_OR_DOWNLOAD_BUTTON&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF32:5384:1AA2DF:2A8C80:5D89D5CB&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/massPix&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="feb178daf028d561781fdecb728675adb64eed2f972f057d3baf0c7428fc2459">
686 Clone or download
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693
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695 Clone with HTTPS
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701 Use Git or checkout with SVN using the web URL.
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707 <clipboard-copy value="https://github.com/wanchanglin/massPix.git" aria-label="Copy to clipboard" class="btn btn-sm" data-hydro-click="{&quot;event_type&quot;:&quot;clone_or_download.click&quot;,&quot;payload&quot;:{&quot;feature_clicked&quot;:&quot;COPY_URL&quot;,&quot;git_repository_type&quot;:&quot;REPOSITORY&quot;,&quot;repository_id&quot;:130720555,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF32:5384:1AA2DF:2A8C80:5D89D5CB&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/massPix&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="eeb1e5fb5bf43e2f259105b0b223aa0596d3a1a1063ca7ee217b34cddac8b312"><svg class="octicon octicon-clippy" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 13h4v1H2v-1zm5-6H2v1h5V7zm2 3V8l-3 3 3 3v-2h5v-2H9zM4.5 9H2v1h2.5V9zM2 12h2.5v-1H2v1zm9 1h1v2c-.02.28-.11.52-.3.7-.19.18-.42.28-.7.3H1c-.55 0-1-.45-1-1V4c0-.55.45-1 1-1h3c0-1.11.89-2 2-2 1.11 0 2 .89 2 2h3c.55 0 1 .45 1 1v5h-1V6H1v9h10v-2zM2 5h8c0-.55-.45-1-1-1H8c-.55 0-1-.45-1-1s-.45-1-1-1-1 .45-1 1-.45 1-1 1H3c-.55 0-1 .45-1 1z"/></svg></clipboard-copy>
708 </div>
709 </div>
710
711 </div>
712
713 <div class="mt-2">
714
715 <a class="btn btn-outline get-repo-btn js-anon-download-zip-link " rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;clone_or_download.click&quot;,&quot;payload&quot;:{&quot;feature_clicked&quot;:&quot;DOWNLOAD_ZIP&quot;,&quot;git_repository_type&quot;:&quot;REPOSITORY&quot;,&quot;repository_id&quot;:130720555,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF32:5384:1AA2DF:2A8C80:5D89D5CB&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/massPix&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="a664684912fc9b6edd29db06e430548810a0c88a903c1e92383c91031f0b5cf0" data-ga-click="Repository, download zip, location:repo overview" href="/wanchanglin/massPix/archive/master.zip">Download ZIP</a>
716
717 </div>
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720 <div class="js-modal-downloading" hidden>
721 <div class="py-2 px-3">
722 <h4 class="lh-condensed mb-3">Downloading<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
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724 Want to be notified of new releases in
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727 </div>
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729 <a rel="nofollow" class="get-repo-btn btn btn-outline" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:130720555,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF32:5384:1AA2DF:2A8C80:5D89D5CB&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/massPix&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="6915548b44b0d7108a8bf9e7cb47da859e5648e7707a4064f856e68eb6c381a3" href="/login?return_to=https%3A%2F%2Fgithub.com%2Fwanchanglin%2FmassPix">Sign in</a>
730 <a rel="nofollow" class="get-repo-btn btn btn-primary" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:130720555,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF32:5384:1AA2DF:2A8C80:5D89D5CB&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/massPix&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="0a82bcfc1b7171272fec225a6f8f34d65d0086bc596c8fca3b5bfac2f51f5e81" href="/join?return_to=%2Fwanchanglin%2FmassPix">Sign up</a>
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733
734 <div class="js-modal-download-mac py-2 px-3 d-none">
735 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
736 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
737 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
738 </div>
739
740 <div class="js-modal-download-windows py-2 px-3 d-none">
741 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
742 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
743 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
744 </div>
745
746 <div class="js-modal-download-xcode py-2 px-3 d-none">
747 <h4 class="lh-condensed mb-3">Launching Xcode<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
748 <p class="text-gray">If nothing happens, <a href="https://developer.apple.com/xcode/">download Xcode</a> and try again.</p>
749 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
750 </div>
751
752 <div class="js-modal-download-visual-studio py-2 px-3 d-none">
753 <h4 class="lh-condensed mb-3">Launching Visual Studio<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
754 <p class="text-gray">If nothing happens, <a href="https://visualstudio.github.com/">download the GitHub extension for Visual Studio</a> and try again.</p>
755 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
756 </div>
757
758 </div>
759 </div>
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762 </div>
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764
765
766
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769
770 <div class="AvatarStack flex-self-start ">
771 <div class="AvatarStack-body" aria-label="harryln">
772 <a class="avatar" data-skip-pjax="true" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=4497792" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/harryln">
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776
777 <div class="flex-auto f6 mr-3">
778
779 <a href="/wanchanglin/massPix/commits?author=harryln"
780 class="commit-author tooltipped tooltipped-s user-mention"
781 aria-label="View all commits by harryln">harryln</a>
782
783
784
785
786
787 <a data-pjax="true" title="pass all tests" class="message text-inherit" href="/wanchanglin/massPix/commit/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33">pass all tests</a>
788
789 </div>
790 <div class="no-wrap d-flex flex-items-baseline">
791 <span class="mr-1">Latest commit</span>
792 <a class="commit-tease-sha mr-1" href="/wanchanglin/massPix/commit/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33" data-pjax>
793 3dc006d
794 </a>
795 <span itemprop="dateModified"><relative-time datetime="2019-04-06T08:18:00Z">Apr 6, 2019</relative-time></span>
796 </div>
797 </div>
798
799
800
801 <div class="file-wrap">
802 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/wanchanglin/massPix/tree/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33">Permalink</a>
803
804 <table class="files js-navigation-container js-active-navigation-container" data-pjax>
805 <thead>
806 <tr>
807 <th><span class="sr-only">Type</span></th>
808 <th><span class="sr-only">Name</span></th>
809 <th><span class="sr-only">Latest commit message</span></th>
810 <th><span class="sr-only">Commit time</span></th>
811 </tr>
812 </thead>
813
814
815 <tbody>
816 <tr class="warning include-fragment-error">
817 <td class="icon"><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></td>
818 <td class="content" colspan="3">Failed to load latest commit information.</td>
819 </tr>
820
821 <tr class="js-navigation-item">
822 <td class="icon">
823 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
824 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
825 </td>
826 <td class="content">
827 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="imzMLConverter" id="5bce44c3378dbdd4490fda57da232ae3-3a000c804d8cf086e3e5e26e7e3879c25c8ed01b" href="/wanchanglin/massPix/tree/master/imzMLConverter">imzMLConverter</a></span>
828 </td>
829 <td class="message">
830 <span class="css-truncate css-truncate-target">
831 <a data-pjax="true" title="add java stuff" class="link-gray" href="/wanchanglin/massPix/commit/7b043cdbe6ca7e2165b5bf9e17489449f9c7b152">add java stuff</a>
832 </span>
833 </td>
834 <td class="age">
835 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-04-24T14:44:24Z">Apr 24, 2018</time-ago></span>
836 </td>
837 </tr>
838 <tr class="js-navigation-item">
839 <td class="icon">
840 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
841 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
842 </td>
843 <td class="content">
844 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="libraries" id="550d742961671466d104ab3e933c790d-fdc250ee4dd63848e8917cebb42d6b327de8764a" href="/wanchanglin/massPix/tree/master/libraries">libraries</a></span>
845 </td>
846 <td class="message">
847 <span class="css-truncate css-truncate-target">
848 <a data-pjax="true" title="initial" class="link-gray" href="/wanchanglin/massPix/commit/27acc60c19d8e27df14c98d141bbb1b8adecc75e">initial</a>
849 </span>
850 </td>
851 <td class="age">
852 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-04-23T16:19:40Z">Apr 23, 2018</time-ago></span>
853 </td>
854 </tr>
855 <tr class="js-navigation-item">
856 <td class="icon">
857 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
858 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
859 </td>
860 <td class="content">
861 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="test-data" id="24346e1b50066607059af36e3b684b24-214a75655e7643d2023ca498fa2b33279f0b69ec" href="/wanchanglin/massPix/tree/master/test-data">test-data</a></span>
862 </td>
863 <td class="message">
864 <span class="css-truncate css-truncate-target">
865 <a data-pjax="true" title="pass all tests" class="link-gray" href="/wanchanglin/massPix/commit/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33">pass all tests</a>
866 </span>
867 </td>
868 <td class="age">
869 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-06T08:18:00Z">Apr 6, 2019</time-ago></span>
870 </td>
871 </tr>
872 <tr class="js-navigation-item">
873 <td class="icon">
874 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
875 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
876 </td>
877 <td class="content">
878 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="test" id="098f6bcd4621d373cade4e832627b4f6-0a7a6f9bebd293eeaad809f49bfad9edf02744a3" href="/wanchanglin/massPix/tree/master/test">test</a></span>
879 </td>
880 <td class="message">
881 <span class="css-truncate css-truncate-target">
882 <a data-pjax="true" title="pass all tests" class="link-gray" href="/wanchanglin/massPix/commit/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33">pass all tests</a>
883 </span>
884 </td>
885 <td class="age">
886 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-06T08:18:00Z">Apr 6, 2019</time-ago></span>
887 </td>
888 </tr>
889 <tr class="js-navigation-item">
890 <td class="icon">
891 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
892 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
893 </td>
894 <td class="content">
895 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title=".gitignore" id="a084b794bc0759e7a6b77810e01874f2-5d165801200f8a83e431365459a3d91bb12fc61c" href="/wanchanglin/massPix/blob/master/.gitignore">.gitignore</a></span>
896 </td>
897 <td class="message">
898 <span class="css-truncate css-truncate-target">
899 <a data-pjax="true" title="add ibd file" class="link-gray" href="/wanchanglin/massPix/commit/6418093acdc3a0def28e7b2f896258bc1cd738c9">add ibd file</a>
900 </span>
901 </td>
902 <td class="age">
903 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-03T15:46:29Z">Apr 3, 2019</time-ago></span>
904 </td>
905 </tr>
906 <tr class="js-navigation-item">
907 <td class="icon">
908 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
909 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
910 </td>
911 <td class="content">
912 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="README.md" id="04c6e90faac2675aa89e2176d2eec7d8-250d08eabccedd6a6a152bc65cfa7265d4b19cdd" href="/wanchanglin/massPix/blob/master/README.md">README.md</a></span>
913 </td>
914 <td class="message">
915 <span class="css-truncate css-truncate-target">
916 <a data-pjax="true" title="README.md and minor changes" class="link-gray" href="/wanchanglin/massPix/commit/cf016f177cc60db75119a2065ddda717004f37ef">README.md and minor changes</a>
917 </span>
918 </td>
919 <td class="age">
920 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-03-28T12:05:58Z">Mar 28, 2019</time-ago></span>
921 </td>
922 </tr>
923 <tr class="js-navigation-item">
924 <td class="icon">
925 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
926 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
927 </td>
928 <td class="content">
929 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="all_massPix.R" id="ed5938c36712249e72b90013e29434e7-da13dfc864a8b34f6bb518226bb061032f616847" href="/wanchanglin/massPix/blob/master/all_massPix.R">all_massPix.R</a></span>
930 </td>
931 <td class="message">
932 <span class="css-truncate css-truncate-target">
933 <a data-pjax="true" title="planemo test" class="link-gray" href="/wanchanglin/massPix/commit/a477d99ba1bc4b370f2aa1d262d069adcdc21b28">planemo test</a>
934 </span>
935 </td>
936 <td class="age">
937 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-03-25T17:04:03Z">Mar 25, 2019</time-ago></span>
938 </td>
939 </tr>
940 <tr class="js-navigation-item">
941 <td class="icon">
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943 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
944 </td>
945 <td class="content">
946 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="macros.xml" id="f14f3135d9f740d9fd0c76a73eb879c0-38f3634a23683a43c1ac6f918b8d83ca52e53b4e" href="/wanchanglin/massPix/blob/master/macros.xml">macros.xml</a></span>
947 </td>
948 <td class="message">
949 <span class="css-truncate css-truncate-target">
950 <a data-pjax="true" title="planemo test for new data" class="link-gray" href="/wanchanglin/massPix/commit/784c4a268b00f0aa8fd4013bb50d623891b1298a">planemo test for new data</a>
951 </span>
952 </td>
953 <td class="age">
954 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-05T11:21:12Z">Apr 5, 2019</time-ago></span>
955 </td>
956 </tr>
957 <tr class="js-navigation-item">
958 <td class="icon">
959 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
960 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
961 </td>
962 <td class="content">
963 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="massPix.R" id="a6acca5d8bc93b8872e3d82a700c0184-36777e1788959d16a6c9d92e59d30f3e9d0c5236" href="/wanchanglin/massPix/blob/master/massPix.R">massPix.R</a></span>
964 </td>
965 <td class="message">
966 <span class="css-truncate css-truncate-target">
967 <a data-pjax="true" title="planemo test and add &#39;set.seed&#39; in R script" class="link-gray" href="/wanchanglin/massPix/commit/6f1e4cdfd93bfc245fcfdc956f08b896e9230c53">planemo test and add 'set.seed' in R script</a>
968 </span>
969 </td>
970 <td class="age">
971 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-05T16:49:33Z">Apr 5, 2019</time-ago></span>
972 </td>
973 </tr>
974 <tr class="js-navigation-item">
975 <td class="icon">
976 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
977 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
978 </td>
979 <td class="content">
980 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="massPix.xml" id="d7a30f4ba39aeab55a58b131e565f40a-20cbeffb7c85b40ae5a1805d762d858724c4d8ce" href="/wanchanglin/massPix/blob/master/massPix.xml">massPix.xml</a></span>
981 </td>
982 <td class="message">
983 <span class="css-truncate css-truncate-target">
984 <a data-pjax="true" title="pass all tests" class="link-gray" href="/wanchanglin/massPix/commit/3dc006dbd0a9058576d9f3be4ea870ce79cbaf33">pass all tests</a>
985 </span>
986 </td>
987 <td class="age">
988 <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-06T08:18:00Z">Apr 6, 2019</time-ago></span>
989 </td>
990 </tr>
991 </tbody>
992 </table>
993
994 </div>
995
996
997
998 <div id="readme" class="Box Box--condensed instapaper_body md js-code-block-container">
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1018
1019 <div class="Box-body">
1020 <article class="markdown-body entry-content p-5" itemprop="text"><h1><a id="user-content-masspix-for-galaxy" class="anchor" aria-hidden="true" href="#masspix-for-galaxy"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>massPix for Galaxy</h1>
1021 <p>This is Galaxy tool for R package <code>massPix</code> which processes high resolution
1022 mass spectrometry imaging data, performs multivariate statistics (PCA,
1023 clustering) and lipid identification. For details, see
1024 <a href="https://github.com/hallz/massPix">R package massPix</a> and <a href="https://link.springer.com/article/10.1007%2Fs11306-017-1252-5" rel="nofollow">Metabolomics
1025 publication</a>.</p>
1026 <h2><a id="user-content-installation" class="anchor" aria-hidden="true" href="#installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Installation</h2>
1027 <ul>
1028 <li>
1029 <p>Install <a href="https://github.com/galaxyproject/galaxy">Galaxy</a> under Linux.</p>
1030 </li>
1031 <li>
1032 <p>Install <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow">conda</a> under
1033 Linux. <code>conda</code> is used to install <code>requirements</code> of this tool.</p>
1034 </li>
1035 <li>
1036 <p>Use <code>git</code> to clone this tool</p>
1037 <div class="highlight highlight-source-shell"><pre>git clone https://github.com/wanchanglin/massPix.git</pre></div>
1038 </li>
1039 <li>
1040 <p>Add this tool's location into Galaxy' tool config file:
1041 <code>~/Galaxy/config/tool_conf.xml</code>. For example, one simplified
1042 <code>tool_conf.xml</code> looks like:</p>
1043 <div class="highlight highlight-text-xml"><pre>&lt;?<span class="pl-ent">xml</span><span class="pl-e"> version</span>=<span class="pl-s"><span class="pl-pds">'</span>1.0<span class="pl-pds">'</span></span><span class="pl-e"> encoding</span>=<span class="pl-s"><span class="pl-pds">'</span>utf-8<span class="pl-pds">'</span></span>?&gt;
1044 &lt;<span class="pl-ent">toolbox</span> <span class="pl-e">monitor</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>&gt;
1045
1046 &lt;<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>getext<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>Get Data<span class="pl-pds">"</span></span>&gt;
1047 &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>data_source/upload.xml<span class="pl-pds">"</span></span> /&gt;
1048 &lt;/<span class="pl-ent">section</span>&gt;
1049
1050 &lt;<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>MyTools<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>My Tools<span class="pl-pds">"</span></span>&gt;
1051 &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>/path/to/massPix/massPix.xml<span class="pl-pds">"</span></span> /&gt;
1052 &lt;/<span class="pl-ent">section</span>&gt;
1053
1054 &lt;/<span class="pl-ent">toolbox</span>&gt;</pre></div>
1055 </li>
1056 <li>
1057 <p>The Galaxy tool uses <a href="https://cran.r-project.org/" rel="nofollow">R</a> packages <code>optparse</code>,
1058 <code>WriteXLS</code>, <code>calibrate</code> and <code>rJava</code>. This tool embeds a modified
1059 <code>massPix</code> package for Galaxy only.</p>
1060 </li>
1061 <li>
1062 <p>To test the tool, use data inside <code>test-data</code> or download test data (.ibd
1063 and .imzML files) from the
1064 <a href="https://www.ebi.ac.uk/metabolights/" rel="nofollow">MetaboLights</a> repository accession
1065 number <a href="https://www.ebi.ac.uk/metabolights/MTBLS487" rel="nofollow">MTBLS487</a>.</p>
1066 </li>
1067 </ul>
1068 <h2><a id="user-content-authors-contributors--contacts" class="anchor" aria-hidden="true" href="#authors-contributors--contacts"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Authors, contributors &amp; contacts</h2>
1069 <ul>
1070 <li>Wanchang Lin (<a href="mailto:wl361@cam.ac.uk">wl361@cam.ac.uk</a>), University of Cambridge</li>
1071 <li>Zoe Hall (<a href="mailto:zlh22@cam.ac.uk">zlh22@cam.ac.uk</a>), University of Cambridge</li>
1072 <li>Julian L Griffin (<a href="mailto:jlg40@cam.ac.uk">jlg40@cam.ac.uk</a>), University of Cambridge</li>
1073 </ul>
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