# HG changeset patch
# User ebi-gxa
# Date 1594432366 14400
# Node ID fd0fc93b3c874783af3a43f1df045e7e23461437
# Parent  13a27436f8eeb63407cf6d0b3aeb156b2eec1556
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0

diff -r 13a27436f8ee -r fd0fc93b3c87 seurat_macros.xml
--- a/seurat_macros.xml	Mon Nov 25 06:11:40 2019 -0500
+++ b/seurat_macros.xml	Fri Jul 10 21:52:46 2020 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.0.6</token>
+    <token name="@VERSION@">0.0.7</token>
     <token name="@SEURAT_VERSION@">3.1.1</token>
     <xml name="requirements">
         <requirements>
@@ -97,6 +97,8 @@
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+3.1.1_0.0.7: Exposes perplexity and enables tab input.
+
 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
 
   Find clusters: removed dims-use, k-param, prune-snn.
@@ -121,6 +123,7 @@
               url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
             }
             </citation>
+            <citation type="doi">10.1101/2020.04.08.032698</citation>
         </citations>
     </xml>
 </macros>
diff -r 13a27436f8ee -r fd0fc93b3c87 seurat_run_tsne.xml
--- a/seurat_run_tsne.xml	Mon Nov 25 06:11:40 2019 -0500
+++ b/seurat_run_tsne.xml	Fri Jul 10 21:52:46 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
+<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@+galaxy1">
     <description>run t-SNE dimensionality reduction</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -31,6 +31,9 @@
 #if $adv.random_seed
   --random-seed '$adv.random_seed'
 #end if
+#if $adv.perplexity
+  --perplexity '$adv.perplexity'
+#end if
 
 @OUTPUT_OBJECT@
 --output-embeddings-file output_embed
@@ -51,6 +54,7 @@
               <option value="2" selected="true">2</option>
               <option value="3">3</option>
             </param>
+            <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/>
             <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
         </section>
     </inputs>