changeset 0:77457f03804a draft

Uploaded
author metaboflow_cam
date Tue, 22 Oct 2019 03:48:52 -0400
parents
children b8b3148de013
files dimsp
diffstat 1 files changed, 1174 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dimsp	Tue Oct 22 03:48:52 2019 -0400
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+                    <h4 class="text-gray-light text-normal text-mono f5 mb-2  border-top pt-3">Connect with others</h4>
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+              <li class=" mr-3 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
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+            class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1"
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+      Security
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+  <div class="repository-content ">
+
+    
+    
+        <div class="signup-prompt-bg rounded-1">
+      <div class="signup-prompt p-4 text-center mb-4 rounded-1">
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+          <a class="btn btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;files signup prompt&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="c2c3b9a7486f9c09acd21f560ef5dea90639f1e62f0d5b686c0c3d2554cae66f" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-code&amp;source_repo=wanchanglin%2Fdimsp">Sign up</a>
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+  <div class="overall-summary overall-summary-bottomless">
+    <ul class="numbers-summary">
+      <li class="commits">
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+            <span class="num text-emphasized">
+              50
+            </span>
+            commits
+        </a>
+      </li>
+      <li>
+        <a data-pjax href="/wanchanglin/dimsp/branches">
+          <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 00-1 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 00-1-3.72C.88 1 0 1.89 0 3a2 2 0 001 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>
+          <span class="num text-emphasized">
+            1
+          </span>
+          branch
+        </a>
+      </li>
+
+
+      <li>
+        <a href="/wanchanglin/dimsp/releases">
+          <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 0 000-1.41L7.73 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>
+          <span class="num text-emphasized">
+            0
+          </span>
+          releases
+        </a>
+      </li>
+
+
+        <li >
+            <include-fragment src="/wanchanglin/dimsp/contributors_size">
+              <a href="/wanchanglin/dimsp/graphs/contributors">
+                <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>
+                <span class="num text-emphasized"></span>
+                Fetching contributors
+              </a>
+</include-fragment>        </li>
+
+    </ul>
+  </div>
+
+    <details class="details-reset">
+      <summary title="Click for language details" data-ga-click="Repository, language bar stats toggle, location:repo overview">
+        <div class="d-flex repository-lang-stats-graph">
+            <span class="language-color" aria-label="R 91.7%" style="width:91.7%; background-color:#198CE7;" itemprop="keywords">R</span>
+            <span class="language-color" aria-label="Shell 8.3%" style="width:8.3%; background-color:#89e051;" itemprop="keywords">Shell</span>
+        </div>
+      </summary>
+      <div class="repository-lang-stats">
+        <ol class="repository-lang-stats-numbers">
+          <li>
+              <a href="/wanchanglin/dimsp/search?l=r"  data-ga-click="Repository, language stats search click, location:repo overview">
+                <span class="color-block language-color" style="background-color:#198CE7;"></span>
+                <span class="lang">R</span>
+                <span class="percent">91.7%</span>
+              </a>
+          </li>
+          <li>
+              <a href="/wanchanglin/dimsp/search?l=shell"  data-ga-click="Repository, language stats search click, location:repo overview">
+                <span class="color-block language-color" style="background-color:#89e051;"></span>
+                <span class="lang">Shell</span>
+                <span class="percent">8.3%</span>
+              </a>
+          </li>
+        </ol>
+      </div>
+    </details>
+
+
+
+
+
+
+  <div class="file-navigation in-mid-page d-flex flex-items-start">
+  
+<details class="details-reset details-overlay select-menu branch-select-menu  hx_rsm" id="branch-select-menu">
+  <summary class="btn btn-sm select-menu-button css-truncate"
+           data-hotkey="w"
+           title="Switch branches or tags">
+    <i>Branch:</i>
+    <span class="css-truncate-target" data-menu-button>master</span>
+  </summary>
+
+  <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/wanchanglin/dimsp/ref-list/master?source_action=disambiguate&amp;source_controller=files" preload>
+    <include-fragment class="select-menu-loading-overlay anim-pulse">
+      <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg>
+    </include-fragment>
+  </details-menu>
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+          New pull request
+        </button>
+
+  <div class="breadcrumb flex-auto">
+    
+  </div>
+
+  <div class="BtnGroup">
+
+
+    <a class="btn btn-sm empty-icon float-right BtnGroup-item" data-hydro-click="{&quot;event_type&quot;:&quot;repository.click&quot;,&quot;payload&quot;:{&quot;target&quot;:&quot;FIND_FILE_BUTTON&quot;,&quot;repository_id&quot;:143855043,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="9a64439aed80123e65a5ff232206f799e9d2bef523e3a63d08b1833d5d92c899" data-ga-click="Repository, find file, location:repo overview" data-hotkey="t" data-pjax="true" href="/wanchanglin/dimsp/find/master">Find file</a>
+  </div>
+
+
+    
+
+    <details class="get-repo-select-menu js-get-repo-select-menu js-anon-get-repo-select-menu position-relative details-overlay details-reset">
+  <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;:143855043,&quot;target&quot;:&quot;CLONE_OR_DOWNLOAD_BUTTON&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="d33835c6b1b5b069187abc93e012732c17d26e0fecfb7df7899079b5f7dc53a1">
+    Clone or download
+    <span class="dropdown-caret"></span>
+</summary>  <div class="position-relative">
+    <div class="get-repo-modal dropdown-menu dropdown-menu-sw pb-0 js-toggler-container  js-get-repo-modal">
+
+      <div class="get-repo-modal-options">
+          <div class="clone-options https-clone-options">
+
+            <h4 class="mb-1">
+              Clone with HTTPS
+              <a class="muted-link" href="https://help.github.com/articles/which-remote-url-should-i-use" target="_blank" title="Which remote URL should I use?">
+                <svg class="octicon octicon-question" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 10h2v2H6v-2zm4-3.5C10 8.64 8 9 8 9H6c0-.55.45-1 1-1h.5c.28 0 .5-.22.5-.5v-1c0-.28-.22-.5-.5-.5h-1c-.28 0-.5.22-.5.5V7H4c0-1.5 1.5-3 3-3s3 1 3 2.5zM7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 011.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7z"/></svg>
+              </a>
+            </h4>
+            <p class="mb-2 get-repo-decription-text">
+              Use Git or checkout with SVN using the web URL.
+            </p>
+
+            <div class="input-group">
+  <input type="text" class="form-control input-monospace input-sm" data-autoselect value="https://github.com/wanchanglin/dimsp.git" aria-label="Clone this repository at https://github.com/wanchanglin/dimsp.git" readonly>
+  <div class="input-group-button">
+    <clipboard-copy value="https://github.com/wanchanglin/dimsp.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;:143855043,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="63d239fe0c92f11739d2517dfd563dcf2ac529d59aee24f5773c23e165bf2779"><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>
+  </div>
+</div>
+
+          </div>
+
+        <div class="mt-2">
+          
+<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;:143855043,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="35b39741b5a3e31e07510a718f2b5642a19b1b6fc0aa8e1f54a2216121979c51" data-ga-click="Repository, download zip, location:repo overview" href="/wanchanglin/dimsp/archive/master.zip">Download ZIP</a>
+
+        </div>
+      </div>
+
+        <div class="js-modal-downloading" hidden>
+          <div class="py-2 px-3">
+            <h4 class="lh-condensed mb-3">Downloading<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
+            <p class="text-gray">
+              Want to be notified of new releases in
+              <span class="text-bold">wanchanglin/dimsp</span>?
+            </p>
+          </div>
+          <div class="width-full d-flex">
+            <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;:143855043,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="82bb27c932d6cd246bcf18a42fd4d0585b9859fbfc4317f00249c0fe91d8d253" href="/login?return_to=https%3A%2F%2Fgithub.com%2Fwanchanglin%2Fdimsp">Sign in</a>
+              <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;:143855043,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9FFE:4E1D:338843:60050C:5DAEB463&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/dimsp&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="287a736b6a427d08145fcd8cc4c379013a43089681cd70cb02d8b5dab6d7bebe" href="/join?return_to=%2Fwanchanglin%2Fdimsp">Sign up</a>
+          </div>
+        </div>
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+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="test" id="098f6bcd4621d373cade4e832627b4f6-fc91d9fa558358f7b8e229096a15a2eb82b82854" href="/wanchanglin/dimsp/tree/master/test">test</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="remove large mzXML test files and pass planemo tests" class="link-gray" href="/wanchanglin/dimsp/commit/1b22f2b60b928be5d1faa32961808cc5d62c1657">remove large mzXML test files and pass planemo tests</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-10-06T16:53:08Z" class="no-wrap">Oct 6, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
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+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="planemo test again" class="link-gray" href="/wanchanglin/dimsp/commit/d54cf8a72a6b3fe65702551d89c0515d71e85c1c">planemo test again</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-10-11T09:26:51Z" class="no-wrap">Oct 11, 2019</time-ago></span>
+          </td>
+        </tr>
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+          <td class="icon">
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+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
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+          <td class="content">
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+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="debug RSD threshold for QC filtering and pass all &#39;planemo test&#39;" class="link-gray" href="/wanchanglin/dimsp/commit/eb248043d5e44c5e75727f06f9a33637f16fbc32">debug RSD threshold for QC filtering and pass all 'planemo test'</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-01T11:43:59Z" class="no-wrap">Apr 1, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
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+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="all_dimsp.R" id="7172d35813d6a3823e4d499bc4de8ba3-8f18592263b8f485fd7b0e15106acf43201a9963" href="/wanchanglin/dimsp/blob/master/all_dimsp.R">all_dimsp.R</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="tidy up and add mzML input" class="link-gray" href="/wanchanglin/dimsp/commit/c6267626a0b7cb9d010220bc8dacbf007ebe7cf8">tidy up and add mzML input</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-03-01T12:45:17Z" class="no-wrap">Mar 1, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
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+          <td class="content">
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+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="more comments on dimsp.R" class="link-gray" href="/wanchanglin/dimsp/commit/4cd64abd17ddb6189de85a3ad5938e1ed6931e98">more comments on dimsp.R</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-07-19T08:20:22Z" class="no-wrap">Jul 19, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="dimsp.xml" id="32d7d005ee7a44396b8d4035cb2513ef-5a26e94d3247ab3ee48222196a0b00e45a8b0555" href="/wanchanglin/dimsp/blob/master/dimsp.xml">dimsp.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="remove large mzXML test files and pass planemo tests" class="link-gray" href="/wanchanglin/dimsp/commit/1b22f2b60b928be5d1faa32961808cc5d62c1657">remove large mzXML test files and pass planemo tests</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-10-06T16:53:08Z" class="no-wrap">Oct 6, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="dimsp_filter.R" id="acce1d2b1bbbd43ccfcdb30268a9678e-57ae04ef63ac4dcdaf6261729d176b818d311972" href="/wanchanglin/dimsp/blob/master/dimsp_filter.R">dimsp_filter.R</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="debug RSD threshold for QC filtering and pass all &#39;planemo test&#39;" class="link-gray" href="/wanchanglin/dimsp/commit/eb248043d5e44c5e75727f06f9a33637f16fbc32">debug RSD threshold for QC filtering and pass all 'planemo test'</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-04-01T11:43:59Z" class="no-wrap">Apr 1, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="dimsp_filter.xml" id="26443f7e48cf6a0994915cdbc1e2e391-bd6292a839fa37fe7de60d2610adf96781df54b2" href="/wanchanglin/dimsp/blob/master/dimsp_filter.xml">dimsp_filter.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="remove large mzXML test files and pass planemo tests" class="link-gray" href="/wanchanglin/dimsp/commit/1b22f2b60b928be5d1faa32961808cc5d62c1657">remove large mzXML test files and pass planemo tests</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-10-06T16:53:08Z" class="no-wrap">Oct 6, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="fs_filter.R" id="440514a0a568bb961e7748d074953219-adc8fd51d8eef33778ff593a301d1c1182a8b364" href="/wanchanglin/dimsp/blob/master/fs_filter.R">fs_filter.R</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="tidy up and add mzML input" class="link-gray" href="/wanchanglin/dimsp/commit/c6267626a0b7cb9d010220bc8dacbf007ebe7cf8">tidy up and add mzML input</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-03-01T12:45:17Z" class="no-wrap">Mar 1, 2019</time-ago></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <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>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="macros.xml" id="f14f3135d9f740d9fd0c76a73eb879c0-c6d86ad8625d5df8abc5d4de4a548a78a3e5a90f" href="/wanchanglin/dimsp/blob/master/macros.xml">macros.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+                  <a data-pjax="true" title="add version in macro.xml" class="link-gray" href="/wanchanglin/dimsp/commit/dd3aab490fc38c1641a505babc237cdf61137a4c">add version in macro.xml</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time-ago datetime="2019-10-02T15:09:40Z" class="no-wrap">Oct 2, 2019</time-ago></span>
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+        <article class="markdown-body entry-content p-5" itemprop="text"><h1><a id="user-content-dimsp-for-galaxy" class="anchor" aria-hidden="true" href="#dimsp-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>DIMSP for Galaxy</h1>
+<p>Galaxy tool for Direct-Infusion Mass Spectrometry (DIMS) based lipidomics
+data processing and filtering.</p>
+<p>For details how to get annotation and peak table, see
+<a href="https://github.com/hallz/dims_processing">dims_processing</a>.</p>
+<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>
+<ul>
+<li>
+<p>Install <a href="https://github.com/galaxyproject/galaxy">Galaxy</a> under Linux.</p>
+</li>
+<li>
+<p>Install <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow">conda</a> under
+Linux. <code>conda</code> is used to install <code>requirements</code> of this tool, i.e. R
+packages used: <code>optparse</code>, <code>WriteXLS</code>, <code>xcms</code>, <code>data.table</code>,
+<code>reshape</code>, <code>lattice</code>, <code>impute</code> and <code>pcaMethods</code>.</p>
+</li>
+<li>
+<p>Use <code>git</code> to clone this tool</p>
+<div class="highlight highlight-source-shell"><pre>git clone https://github.com/wanchanglin/dimsp.git</pre></div>
+</li>
+<li>
+<p>Add this tool's location into Galaxy' tool config file:
+<code>~/Galaxy/config/tool_conf.xml</code>. For example, one simplified
+<code>tool_conf.xml</code> looks like:</p>
+<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;
+&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;
+  
+  &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;
+    &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;
+  &lt;/<span class="pl-ent">section</span>&gt;
+  
+  &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;
+    &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>/path/to/dimsp/dimsp.xml<span class="pl-pds">"</span></span> /&gt;
+    &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>/path/to/dimsp/dimsp_filter.xml<span class="pl-pds">"</span></span> /&gt;
+  &lt;/<span class="pl-ent">section</span>&gt;
+
+&lt;/<span class="pl-ent">toolbox</span>&gt;</pre></div>
+</li>
+<li>
+<p>Test data are in <code>test-data</code>, includes:</p>
+<ul>
+<li>mzXML and mzML files for DIMSP processing.</li>
+<li>Lipid lists in TSV(Tab Separated Values) format.</li>
+<li>TSV files for DIMSP filtering.</li>
+</ul>
+</li>
+</ul>
+<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>
+<ul>
+<li>Wanchang Lin (<a href="mailto:wl361@cam.ac.uk">wl361@cam.ac.uk</a>), University of Cambridge</li>
+<li>Zoe Hall (<a href="mailto:zlh22@cam.ac.uk">zlh22@cam.ac.uk</a>), University of Cambridge</li>
+<li>Julian L Griffin (<a href="mailto:jlg40@cam.ac.uk">jlg40@cam.ac.uk</a>), University of Cambridge</li>
+</ul>
+</article>
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