--- a/music_compare.xml	Thu Feb 10 12:53:49 2022 +0000
+++ b/music_compare.xml	Mon May 02 09:58:49 2022 +0000
@@ -31,6 +31,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code" ><![CDATA[
+cat '$conf' >> /dev/stderr &&
 mkdir report_data &&
 Rscript --vanilla '$__tool_directory__/scripts/compare.R' '$conf'
 ]]></command>
@@ -77,10 +78,11 @@
 #end for
 )
 
-heat_grouped_p = as.logical('$heat_grouped_p')
 out_filt = list(cells = null_str_vec('$filter.out_list_cells'),
                 facts = null_str_vec('$filter.out_list_facts'))
+
 est_method = null_str_vec('$est_method')
+dendro_setting = null_str_vec('$dendro_setting')
 
 out_heatmulti_pdf = '$out_heatmulti_pdf'
 out_heatsumm_pdf = '$out_heatsumm_pdf'
@@ -132,7 +134,13 @@
             <option value="MuSiC" selected="true" >MuSiC</option>
             <option value="NNLS" selected="true" >NNLS</option>
         </param>
-        <param name="heat_grouped_p" type="boolean" label="Individual heatmaps grouped by scRNA dataset?" checked="true" />
+        <param name="dendro_setting" type="select" label="Cluster heatmaps?"
+               help="Samples, Cells and Datasets can all be clustered by similarity.">
+            <option value="None" selected="true" >No, preserve order of Rows and Columns</option>
+            <option value="Both">Cluster both Rows and Columns</option>
+            <option value="Cols">Cluster only Columns</option>
+            <option value="Rows">Cluster only Rows</option>
+        </param>
         <section name="filter" title="Filter Summary Plots" >
             <param name="out_list_cells" type="text" label="Show only these cell types (blank for all)"
                    help="Comma-delimited list. Cell types given in the above scRNA datasets are still used for deconvolution (bulk reads are still assigned to discrete cell types), but we merely select the ones we want to show." />
@@ -155,7 +163,6 @@
             <!-- NNLS Test with severe output filtering -->
             <expand macro="test_input" />
             <param name="est_method" value="NNLS" />
-            <param name="heat_grouped_p" value="true" />
             <section name="filter" >
                 <param name="out_list_cells" value="PT,Podo,Fib,Endo" />
                 <param name="out_list_facts" value="APOL1,Pheno1" />
@@ -166,7 +173,16 @@
             <!-- NNLS Test with only factor filtering -->
             <expand macro="test_input" />
             <param name="est_method" value="NNLS" />
-            <param name="heat_grouped_p" value="true" />
+            <section name="filter" >
+                <param name="out_list_facts" value="APOL1,Pheno1" />
+            </section>
+            <output name="out_heatmulti_pdf" value="out_heat2.pdf" compare="sim_size" />
+        </test>
+        <test expect_num_outputs="4" >
+            <!-- NNLS Test with factor filtering and dendrograms -->
+            <expand macro="test_input" />
+            <param name="est_method" value="NNLS" />
+            <param name="dendro_setting" value="Both" />
             <section name="filter" >
                 <param name="out_list_facts" value="APOL1,Pheno1" />
             </section>
@@ -176,7 +192,6 @@
             <!-- MuSiC Test with no filtering -->
             <expand macro="test_input" />
             <param name="est_method" value="MuSiC" />
-            <param name="heat_grouped_p" value="true" />
             <output_collection name="dtables" count="3">
                 <element name="Data Table" ftype="tabular" >
                     <assert_contents>