--- a/seurat.xml	Mon Jun 08 17:40:51 2020 -0400
+++ b/seurat.xml	Thu Jul 23 11:22:05 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1">
+<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy2">
     <description>- toolkit for exploration of single-cell RNA-seq data</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.5</token>
@@ -42,6 +42,11 @@
 #else
     #set $heatmaps = 'F'
 #end if
+#if not str($adv.perplexity):
+    #set $adv_perplexity = -1
+#else:
+    #set $adv_perplexity = $adv.perplexity
+#end if
 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
     params = list(counts = \"${counts}\",
         min_cells = \"${adv.min_cells}\",
@@ -51,6 +56,7 @@
         numPCs = \"${adv.num_PCs}\",
         cells_use = \"${adv.cells_use}\",
         resolution = \"${adv.resolution}\",
+        perplexity = \"${adv_perplexity}\",
         min_pct = \"${adv.min_pct}\",
         logfc_threshold = \"${adv.logfc_threshold}\",
         warn = \"${meta.warn}\",
@@ -76,6 +82,7 @@
             <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" />
             <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" />
             <param name="resolution" type="float" value="0.6" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities." />
+            <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" />
             <param name="min_pct" type="float" value="0.1" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" />
             <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold"
                 help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale)between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals." />
@@ -119,6 +126,28 @@
             </section>
             <output name="out_html" ftype="html" value="out.html" compare="sim_size" delta="20000" />
         </test>
+        <test> <!-- perplexity test -->
+            <param name="counts" ftype="tabular" value="counts.tab.gz"/>
+            <section name="adv">
+                <param name="numPCs" value="10" />
+                <param name="min_cells" value="3"/>
+                <param name="min_genes" value="200"/>
+                <param name="low_thresholds" value="1" />
+                <param name="high_thresholds" value="20000000" />
+                <param name="cells_use" value="500"/>
+                <param name="resolution" value="0.6" />
+                <param name="perplexity" value="16" />
+                <param name="min_pct" value="0.25" />
+                <param name="logfc_threshold" value="0.25" />
+            </section>
+            <section name="meta">
+                <param name="showcode" value="T"/>
+                <param name="warn" value="F"/>
+                <param name="varstate" value="F"/>
+                <param name="plots" value="feat"/>
+            </section>
+            <output name="out_html" ftype="html" value="out.html" compare="sim_size" delta="20000" />
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark