changeset 0:6195ef2417aa draft

Uploaded
author metaboflow_cam
date Tue, 24 Sep 2019 04:56:37 -0400
parents
children 1f2508f5423a
files isolab
diffstat 1 files changed, 1131 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isolab	Tue Sep 24 04:56:37 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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+      Security
+</a>
+    <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse people /wanchanglin/isolab/pulse" href="/wanchanglin/isolab/pulse">
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+<div class="container-lg clearfix new-discussion-timeline experiment-repo-nav  px-3">
+  <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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+          <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="&#x2713;" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="Sy6U9HN+kGeCdZ/psTOpcW/3cmWeVu/Y0eKxDfx+az0OfK2/vUP8AF0OLybQY+TfXskRY7PHKxV+DkjcrNp1EQ==" />
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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;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="974768b8d0a0188cf5cacd94743debbe4acf691556cc32bf3178f45d6dee36c5" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-code">Sign up</a>
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+        </em>
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+  <div class="overall-summary overall-summary-bottomless">
+    <ul class="numbers-summary">
+      <li class="commits">
+        <a data-pjax href="/wanchanglin/isolab/commits/master">
+            <svg class="octicon octicon-history" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 13H6V6h5v2H8v5zM7 1C4.81 1 2.87 2.02 1.59 3.59L0 2v4h4L2.5 4.5C3.55 3.17 5.17 2.3 7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-.34.03-.67.09-1H.08C.03 7.33 0 7.66 0 8c0 3.86 3.14 7 7 7s7-3.14 7-7-3.14-7-7-7z"/></svg>
+            <span class="num text-emphasized">
+              49
+            </span>
+            commits
+        </a>
+      </li>
+      <li>
+        <a data-pjax href="/wanchanglin/isolab/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 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>
+          <span class="num text-emphasized">
+            1
+          </span>
+          branch
+        </a>
+      </li>
+
+
+      <li>
+        <a href="/wanchanglin/isolab/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 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>
+          <span class="num text-emphasized">
+            0
+          </span>
+          releases
+        </a>
+      </li>
+
+
+        <li >
+            <a href="/wanchanglin/isolab/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">
+      2
+    </span>
+    contributors
+</a>
+        </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 96.8%" style="width:96.8%; background-color:#198CE7;" itemprop="keywords">R</span>
+            <span class="language-color" aria-label="Shell 3.2%" style="width:3.2%; background-color:#89e051;" itemprop="keywords">Shell</span>
+        </div>
+      </summary>
+      <div class="repository-lang-stats">
+        <ol class="repository-lang-stats-numbers">
+          <li>
+              <a href="/wanchanglin/isolab/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">96.8%</span>
+              </a>
+          </li>
+          <li>
+              <a href="/wanchanglin/isolab/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">3.2%</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/isolab/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>
+</details>
+
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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;:132626836,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="3f8e985b6a3f66c0a20094aa782a2b2453a4b021f7e68146b3b815245874ac43" data-ga-click="Repository, find file, location:repo overview" data-hotkey="t" data-pjax="true" href="/wanchanglin/isolab/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;:132626836,&quot;target&quot;:&quot;CLONE_OR_DOWNLOAD_BUTTON&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="b6727d95e7b3d2e5b04dfbf2336ad836d7e501bcf0ea0eee4ea70c2e095f25f4">
+    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 0 1 1.3 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/isolab.git" aria-label="Clone this repository at https://github.com/wanchanglin/isolab.git" readonly>
+  <div class="input-group-button">
+    <clipboard-copy value="https://github.com/wanchanglin/isolab.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;:132626836,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="d75b2cd61fef65cc896e9cc034c975dac9e3b49f493589679bee33eaa84fa64c"><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;:132626836,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="3f8d17cade212500993a655a6a9e96538550aefe3ed525fbf8f6796695210e65" data-ga-click="Repository, download zip, location:repo overview" href="/wanchanglin/isolab/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/isolab</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;:132626836,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="ef32c00babec7e5282c6049e047a8337dace915956aca2736f976284ee2f7751" href="/login?return_to=https%3A%2F%2Fgithub.com%2Fwanchanglin%2Fisolab">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;:132626836,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;DF72:73F6:96CE7:EEB59:5D89DA44&quot;,&quot;originating_url&quot;:&quot;https://github.com/wanchanglin/isolab&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="b11216ccf87e3d1a208576e45c109334d76d9c66b47cc6d84b79837c72ae8de3" href="/join?return_to=%2Fwanchanglin%2Fisolab">Sign up</a>
+          </div>
+        </div>
+
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+        <article class="markdown-body entry-content p-5" itemprop="text"><h1><a id="user-content-isolab-for-galaxy" class="anchor" aria-hidden="true" href="#isolab-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>isolab for Galaxy</h1>
+<p>This is Galaxy tool for R package
+<a href="https://github.com/RuggeroFerrazza/IsotopicLabelling">IsotopicLabelling</a>
+which analyses mass spectrometric isotopic patterns obtained following
+isotopic labelling experiments. For more details, see the
+<a href="https://academic.oup.com/bioinformatics/article/33/2/300/2525697" rel="nofollow">IsotopicLabelling: an R package for the analysis of MS isotopic patterns of
+labelled
+analytes</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.</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/isolab.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/isolab/isolab.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>The Galaxy tool uses <a href="https://cran.r-project.org/" rel="nofollow">R</a> packages <code>optparse</code>,
+<code>WriteXLS</code> and <code>gsubfn</code>.  All of these packages will be installed by
+<code>conda</code> in its virtual environment. Two R packages <code>IsotopicLabelling</code> and
+<code>ecipes</code> are already included.</p>
+</li>
+<li>
+<p>Some test data are located in <code>test-data</code>.</p>
+</li>
+</ul>
+<h2><a id="user-content-notes" class="anchor" aria-hidden="true" href="#notes"><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>Notes</h2>
+<ul>
+<li><code>planemo test</code> compares the history results in <code>test-data/res</code> produced by
+shell scripts in <code>test</code>. (27-03-2019, Wed)</li>
+<li>White spaces in <code>groups</code> input: Group factor delimiter is comma. No any
+extra white spaces are allowed otherwise an error will be encountered.
+Note that <code>isolab.sh</code> has no problem with white spaces. Probably it is
+'Cheetah' or Galaxy's text input problem. (31-05-2018, Thu)</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>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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