From 7214bf03399289b82aca60404a7065e6006b1613 Mon Sep 17 00:00:00 2001
From: CameronFRWatson <watsocam@ohsu.edu>
Date: Thu, 12 Sep 2024 13:08:20 -0700
Subject: [PATCH] CELESTA: fix plot_cells variable

---
 tools/celesta/celesta.xml | 16 +++++-----------
 tools/celesta/macros.xml  |  2 +-
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/tools/celesta/celesta.xml b/tools/celesta/celesta.xml
index a6d9d7f..98335b3 100644
--- a/tools/celesta/celesta.xml
+++ b/tools/celesta/celesta.xml
@@ -41,14 +41,14 @@
             #if $runmode.options.high_thresholds_file:
                     --highexpthresh '${runmode.options.high_thresholds_file}'
             #end if  
-            #for $p in $plot_cells:
+            #for $p in $runmode.plot_cells:
                 && Rscript '$__tool_directory__/celesta_plot_cells.R'
                     --prior '$prior_info'
                     --celltypes '${p.cell_types}'
-                    --size '$p.test_size' 
-                    --height '$p.height' 
-                    --width '$p.width' 
-                    --dpi '$p.dpi' 
+                    --size '${p.test_size}' 
+                    --height '${p.height}' 
+                    --width '${p.width}' 
+                    --dpi '${p.dpi}' 
             #end for
         #end if
         ]]>
@@ -145,9 +145,6 @@
                     <has_h5_keys keys="obs/celesta_final_cell_type" />
                 </assert_contents>
             </output>
-            <assert_stdout>
-                <has_text text="vasculature 273" />
-            </assert_stdout>
         </test>
         <test expect_num_outputs="3">
             <param name="anndata" value="celesta_image.h5ad" />
@@ -174,9 +171,6 @@
                     <has_size value="1400000" delta="100000" />
                 </assert_contents>
             </output>
-            <assert_stdout>
-                <has_text text="vasculature 168" />
-            </assert_stdout>
         </test>
     </tests>
     <help>
diff --git a/tools/celesta/macros.xml b/tools/celesta/macros.xml
index 38c1efd..aac15ff 100644
--- a/tools/celesta/macros.xml
+++ b/tools/celesta/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.0.0.9</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">20.01</token>
 
     <xml name="celesta_requirements">