Mercurial > repos > iuc > seurat

diff test-data/out.html @ 2:321bdd834266 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
author iuc
date Thu, 19 Dec 2019 02:42:56 -0500
parents 7319f83ae734
children
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--- a/test-data/out.html	Mon Dec 09 14:32:16 2019 -0500
+++ b/test-data/out.html	Thu Dec 19 02:42:56 2019 -0500
@@ -1,18 +1,17 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
 
 <head>
 
 <meta charset="utf-8" />
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
 <meta name="author" content="Performed using Galaxy" />
 
-<meta name="date" content="2019-12-08" />
+<meta name="date" content="2019-12-16" />
 
 <title>Seurat Analysis</title>
 
@@ -332,6 +331,7 @@
   border: none;
   display: inline-block;
   border-radius: 4px;
+  background-color: transparent;
 }
 
 .tabset-dropdown > .nav-tabs.nav-tabs-open > li {
@@ -365,17 +365,17 @@
 
 <h1 class="title toc-ignore">Seurat Analysis</h1>
 <h4 class="author">Performed using Galaxy</h4>
-<h4 class="date">2019-12-08</h4>
+<h4 class="date">2019-12-16</h4>
 
 </div>
 
 
 <pre><code>## [1] &quot;Read in data, generate inital Seurat object&quot;</code></pre>
-<pre class="r"><code>counts &lt;- read.delim(params$counts, row.names=1)
+<pre class="r"><code>counts &lt;- read.delim(params$counts, row.names = 1)
 seuset &lt;- Seurat::CreateSeuratObject(counts = counts, min.cells = min_cells, min.features = min_genes)</code></pre>
 <pre><code>## [1] &quot;Filter and normalize for UMI counts&quot;</code></pre>
 <pre class="r"><code>seuset &lt;- subset(seuset, subset = `nCount_RNA` &gt; low_thresholds &amp; `nCount_RNA` &lt; high_thresholds)
-seuset &lt;- Seurat::NormalizeData(seuset, normalizeation.method = &quot;LogNormalize&quot;, scale.factor = 10000)</code></pre>
+seuset &lt;- Seurat::NormalizeData(seuset, normalization.method = &quot;LogNormalize&quot;, scale.factor = 10000)</code></pre>
 <pre><code>## [1] &quot;Variable Genes&quot;</code></pre>
 <pre class="r"><code>seuset &lt;- Seurat::FindVariableFeatures(object = seuset, selection.method = &quot;mvp&quot;)
 Seurat::VariableFeaturePlot(seuset, cols = c(&quot;black&quot;, &quot;red&quot;), selection.method = &quot;disp&quot;)</code></pre>