diff --git a/tools/tertiary-analysis/scmap/scmap_macros.xml b/tools/tertiary-analysis/scmap/scmap_macros.xml
index a14b4084..ae2e7573 100644
--- a/tools/tertiary-analysis/scmap/scmap_macros.xml
+++ b/tools/tertiary-analysis/scmap/scmap_macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.6.3</token>
+    <token name="@TOOL_VERSION@">1.6.4</token>
     <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.11">scmap-cli</requirement>
+        <requirement type="package" version="0.1.0">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+1.6.4+galaxy0: Update scmap-cli to 0.1.0
 1.6.3+galaxy0: Update scmap-cli to 0.0.11
 1.6.2+galaxy0: Update scmap-cli to 0.0.10
 1.6.1+galaxy0: Update scmap-cli to 0.0.9.
diff --git a/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml b/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
index 72c89efd..30be5044 100644
--- a/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
+++ b/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
@@ -9,6 +9,8 @@
             -i '$index_single_cell_experiment' 
             -p '$project_single_cell_experiment' 
             --number-nearest-neighbours '$n_nearest_neighbours' 
+            --nearest-neighbours-threshold '$nearest_neighbours_threshold'
+            --threshold '$threshold'
             --cluster-col '${cluster_projection.cluster_col}' 
             --output-object-file '$output_single_cell_experiment' 
             --closest-cells-text-file '$closest_cells_text_file' 
@@ -21,6 +23,8 @@
       <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
       <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
       <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" />
+      <param name="nearest_neighbours_threshold" type="integer" label="Nearest neighbour threshold" value='3' help="A positive integer specifying the number of matching nearest neighbours required to label a cell." />
+      <param name="threshold" type="integer" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
      <conditional name="cluster_projection">
         <param name="do_cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>
         <when value="true" >
@@ -43,12 +47,29 @@
         <test>
             <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
             <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
-            <param name="cluster_projection" value="true" />
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
             <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
             <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
             <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
             <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
         </test>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
+            <param name="nearest_neighbours_threshold" value="3" />
+            <param name="threshold" value="0.5" />
+            <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/>
+            <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" />
+            <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/>
+            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
     @HELP@
diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells.csv b/tools/tertiary-analysis/scmap/test-data/closest_cells.csv
new file mode 100644
index 00000000..592f329e
--- /dev/null
+++ b/tools/tertiary-analysis/scmap/test-data/closest_cells.csv
@@ -0,0 +1,6 @@
+,Oocyte..1.RPKM.,Oocyte..2.RPKM.,Oocyte..3.RPKM.,Zygote..1.RPKM.,Zygote..2.RPKM.,Zygote..3.RPKM.,X2.cell.embryo.1..Cell.1.RPKM.,X2.cell.embryo.1..Cell.2.RPKM.,X2.cell.embryo.2..Cell.1.RPKM.,X2.cell.embryo.2..Cell.2.RPKM.,X2.cell.embryo.3..Cell.1.RPKM.,X2.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.1..Cell.1.RPKM.,X4.cell.embryo.1..Cell.2.RPKM.,X4.cell.embryo.1..Cell.3.RPKM.,X4.cell.embryo.1..Cell.4.RPKM.,X4.cell.embryo.2..Cell.1.RPKM.,X4.cell.embryo.2..Cell.2.RPKM.,X4.cell.embryo.2..Cell.3.RPKM.,X4.cell.embryo.2..Cell.4.RPKM.,X4.cell.embryo.3..Cell.1.RPKM.,X4.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.3..Cell.3.RPKM.,X4.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.1..Cell.1.RPKM.,X8.cell.embryo.1..Cell.2.RPKM.,X8.cell.embryo.1..Cell.3.RPKM.,X8.cell.embryo.1..Cell.4.RPKM.,X8.cell.embryo.2..Cell.1.RPKM.,X8.cell.embryo.2..Cell.2.RPKM.,X8.cell.embryo.2..Cell.3.RPKM.,X8.cell.embryo.2..Cell.4.RPKM.,X8.cell.embryo.2..Cell.5.RPKM.,X8.cell.embryo.2..Cell.6.RPKM.,X8.cell.embryo.2..Cell.7.RPKM.,X8.cell.embryo.2..Cell.8.RPKM.,X8.cell.embryo.3..Cell.1.RPKM.,X8.cell.embryo.3..Cell.2.RPKM.,X8.cell.embryo.3..Cell.3.RPKM.,X8.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.3..Cell.5.RPKM.,X8.cell.embryo.3..Cell.6.RPKM.,X8.cell.embryo.3..Cell.7.RPKM.,X8.cell.embryo.3..Cell.8.RPKM.,Morulae..1..Cell.1.RPKM.,Morulae..1..Cell.2.RPKM.,Morulae..1..Cell.3.RPKM.,Morulae..1..Cell.4.RPKM.,Morulae..1..Cell.5.RPKM.,Morulae..1..Cell.6.RPKM.,Morulae..1..Cell.7.RPKM.,Morulae..1..Cell.8.RPKM.,Morulae..2..Cell.1.RPKM.,Morulae..2..Cell.2.RPKM.,Morulae..2..Cell.3.RPKM.,Morulae..2..Cell.4.RPKM.,Morulae..2..Cell.5.RPKM.,Morulae..2..Cell.6.RPKM.,Morulae..2..Cell.7.RPKM.,Morulae..2..Cell.8.RPKM.,Late.blastocyst..1..Cell.1.RPKM.,Late.blastocyst..1..Cell.2.RPKM.,Late.blastocyst..1..Cell.3.RPKM.,Late.blastocyst..1..Cell.4.RPKM.,Late.blastocyst..1..Cell.5.RPKM.,Late.blastocyst..1..Cell.6.RPKM.,Late.blastocyst..1..Cell.7.RPKM.,Late.blastocyst..1..Cell.8.RPKM.,Late.blastocyst..1..Cell.9.RPKM.,Late.blastocyst..1..Cell.10.RPKM.,Late.blastocyst..1..Cell.11.RPKM.,Late.blastocyst..1..Cell.12.RPKM.,Late.blastocyst..2..Cell.1.RPKM.,Late.blastocyst..2..Cell.2.RPKM.,Late.blastocyst..2..Cell.3.RPKM.,Late.blastocyst..2..Cell.4.RPKM.,Late.blastocyst..2..Cell.5.RPKM.,Late.blastocyst..2..Cell.6.RPKM.,Late.blastocyst..2..Cell.7.RPKM.,Late.blastocyst..2..Cell.8.RPKM.,Late.blastocyst..2..Cell.9.RPKM.,Late.blastocyst..2..Cell.10.RPKM.,Late.blastocyst..3..Cell.1.RPKM.,Late.blastocyst..3..Cell.2.RPKM.,Late.blastocyst..3..Cell.3.RPKM.,Late.blastocyst..3..Cell.4.RPKM.,Late.blastocyst..3..Cell.5.RPKM.,Late.blastocyst..3..Cell.6.RPKM.,Late.blastocyst..3..Cell.7.RPKM.,Late.blastocyst..3..Cell.8.RPKM.
+1,1,1,1,6,6,6,10,10,10,10,12,10,23,19,24,22,14,13,24,13,21,24,23,24,28,27,27,25,34,35,36,32,34,34,35,30,37,42,44,38,38,37,39,39,48,49,47,49,46,49,49,27,57,54,55,55,54,51,55,54,62,67,67,63,71,67,62,66,69,69,71,78,65,87,84,78,78,81,82,82,78,81,88,84,90,75,83,78,88,88
+2,2,2,2,11,12,11,7,7,7,7,7,7,13,13,13,14,24,22,14,20,22,23,21,21,27,25,25,27,36,30,30,34,30,33,34,36,38,37,39,39,42,38,43,43,45,46,52,45,51,54,51,26,49,57,56,59,57,59,56,60,70,71,62,67,62,71,69,62,72,62,63,70,76,86,86,81,79,78,76,80,82,82,87,88,89,74,74,88,85,90
+3,3,3,3,12,10,12,8,8,8,8,8,11,14,24,23,21,19,16,19,23,23,18,22,22,26,26,26,26,30,36,34,36,33,36,36,35,40,40,40,41,40,40,38,44,49,54,26,51,54,51,50,28,51,50,59,60,53,58,58,53,61,61,63,64,69,66,64,82,70,70,72,81,71,75,75,76,81,76,78,76,81,78,75,80,88,86,86,90,77,81
+4,6,7,6,4,11,4,9,9,9,9,9,12,24,14,16,16,23,18,23,18,24,13,13,13,40,38,40,38,29,29,29,29,29,29,29,29,42,38,38,37,37,42,37,41,51,50,28,48,50,50,53,47,54,53,54,58,60,56,54,50,71,68,82,65,65,68,67,68,67,65,65,72,73,73,80,82,82,79,79,75,76,79,86,73,85,83,87,89,89,85
+5,5,5,5,5,5,5,12,12,12,12,11,5,22,23,15,24,17,21,17,22,18,22,24,23,25,28,28,28,31,31,31,35,36,35,31,31,41,41,41,40,41,41,41,38,53,51,27,50,49,46,46,52,53,51,58,56,51,55,59,51,65,62,71,72,70,72,66,78,65,72,69,65,70,74,74,79,77,82,77,84,72,76,83,75,72,87,75,85,90,89
diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.rds b/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.rds
new file mode 100644
index 00000000..e4d197ba
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.rds differ
diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv b/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv
new file mode 100644
index 00000000..c9b0d49b
--- /dev/null
+++ b/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv
@@ -0,0 +1,6 @@
+	Oocyte..1.RPKM.	Oocyte..2.RPKM.	Oocyte..3.RPKM.	Zygote..1.RPKM.	Zygote..2.RPKM.	Zygote..3.RPKM.	X2.cell.embryo.1..Cell.1.RPKM.	X2.cell.embryo.1..Cell.2.RPKM.	X2.cell.embryo.2..Cell.1.RPKM.	X2.cell.embryo.2..Cell.2.RPKM.	X2.cell.embryo.3..Cell.1.RPKM.	X2.cell.embryo.3..Cell.2.RPKM.	X4.cell.embryo.1..Cell.1.RPKM.	X4.cell.embryo.1..Cell.2.RPKM.	X4.cell.embryo.1..Cell.3.RPKM.	X4.cell.embryo.1..Cell.4.RPKM.	X4.cell.embryo.2..Cell.1.RPKM.	X4.cell.embryo.2..Cell.2.RPKM.	X4.cell.embryo.2..Cell.3.RPKM.	X4.cell.embryo.2..Cell.4.RPKM.	X4.cell.embryo.3..Cell.1.RPKM.	X4.cell.embryo.3..Cell.2.RPKM.	X4.cell.embryo.3..Cell.3.RPKM.	X4.cell.embryo.3..Cell.4.RPKM.	X8.cell.embryo.1..Cell.1.RPKM.	X8.cell.embryo.1..Cell.2.RPKM.	X8.cell.embryo.1..Cell.3.RPKM.	X8.cell.embryo.1..Cell.4.RPKM.	X8.cell.embryo.2..Cell.1.RPKM.	X8.cell.embryo.2..Cell.2.RPKM.	X8.cell.embryo.2..Cell.3.RPKM.	X8.cell.embryo.2..Cell.4.RPKM.	X8.cell.embryo.2..Cell.5.RPKM.	X8.cell.embryo.2..Cell.6.RPKM.	X8.cell.embryo.2..Cell.7.RPKM.	X8.cell.embryo.2..Cell.8.RPKM.	X8.cell.embryo.3..Cell.1.RPKM.	X8.cell.embryo.3..Cell.2.RPKM.	X8.cell.embryo.3..Cell.3.RPKM.	X8.cell.embryo.3..Cell.4.RPKM.	X8.cell.embryo.3..Cell.5.RPKM.	X8.cell.embryo.3..Cell.6.RPKM.	X8.cell.embryo.3..Cell.7.RPKM.	X8.cell.embryo.3..Cell.8.RPKM.	Morulae..1..Cell.1.RPKM.	Morulae..1..Cell.2.RPKM.	Morulae..1..Cell.3.RPKM.	Morulae..1..Cell.4.RPKM.	Morulae..1..Cell.5.RPKM.	Morulae..1..Cell.6.RPKM.	Morulae..1..Cell.7.RPKM.	Morulae..1..Cell.8.RPKM.	Morulae..2..Cell.1.RPKM.	Morulae..2..Cell.2.RPKM.	Morulae..2..Cell.3.RPKM.	Morulae..2..Cell.4.RPKM.	Morulae..2..Cell.5.RPKM.	Morulae..2..Cell.6.RPKM.	Morulae..2..Cell.7.RPKM.	Morulae..2..Cell.8.RPKM.	Late.blastocyst..1..Cell.1.RPKM.	Late.blastocyst..1..Cell.2.RPKM.	Late.blastocyst..1..Cell.3.RPKM.	Late.blastocyst..1..Cell.4.RPKM.	Late.blastocyst..1..Cell.5.RPKM.	Late.blastocyst..1..Cell.6.RPKM.	Late.blastocyst..1..Cell.7.RPKM.	Late.blastocyst..1..Cell.8.RPKM.	Late.blastocyst..1..Cell.9.RPKM.	Late.blastocyst..1..Cell.10.RPKM.	Late.blastocyst..1..Cell.11.RPKM.	Late.blastocyst..1..Cell.12.RPKM.	Late.blastocyst..2..Cell.1.RPKM.	Late.blastocyst..2..Cell.2.RPKM.	Late.blastocyst..2..Cell.3.RPKM.	Late.blastocyst..2..Cell.4.RPKM.	Late.blastocyst..2..Cell.5.RPKM.	Late.blastocyst..2..Cell.6.RPKM.	Late.blastocyst..2..Cell.7.RPKM.	Late.blastocyst..2..Cell.8.RPKM.	Late.blastocyst..2..Cell.9.RPKM.	Late.blastocyst..2..Cell.10.RPKM.	Late.blastocyst..3..Cell.1.RPKM.	Late.blastocyst..3..Cell.2.RPKM.	Late.blastocyst..3..Cell.3.RPKM.	Late.blastocyst..3..Cell.4.RPKM.	Late.blastocyst..3..Cell.5.RPKM.	Late.blastocyst..3..Cell.6.RPKM.	Late.blastocyst..3..Cell.7.RPKM.	Late.blastocyst..3..Cell.8.RPKM.
+1	1	1	1	6	6	6	10	10	10	10	12	10	23	19	24	22	14	13	24	13	21	24	23	24	28	27	27	25	34	35	36	32	34	34	35	30	37	42	44	38	38	37	39	39	48	49	47	49	46	49	49	27	57	54	55	55	54	51	55	54	62	67	67	63	71	67	62	66	69	69	71	78	65	87	84	78	78	81	82	82	78	81	88	84	90	75	83	78	88	88
+2	2	2	2	11	12	11	7	7	7	7	7	7	13	13	13	14	24	22	14	20	22	23	21	21	27	25	25	27	36	30	30	34	30	33	34	36	38	37	39	39	42	38	43	43	45	46	52	45	51	54	51	26	49	57	56	59	57	59	56	60	70	71	62	67	62	71	69	62	72	62	63	70	76	86	86	81	79	78	76	80	82	82	87	88	89	74	74	88	85	90
+3	3	3	3	12	10	12	8	8	8	8	8	11	14	24	23	21	19	16	19	23	23	18	22	22	26	26	26	26	30	36	34	36	33	36	36	35	40	40	40	41	40	40	38	44	49	54	26	51	54	51	50	28	51	50	59	60	53	58	58	53	61	61	63	64	69	66	64	82	70	70	72	81	71	75	75	76	81	76	78	76	81	78	75	80	88	86	86	90	77	81
+4	6	7	6	4	11	4	9	9	9	9	9	12	24	14	16	16	23	18	23	18	24	13	13	13	40	38	40	38	29	29	29	29	29	29	29	29	42	38	38	37	37	42	37	41	51	50	28	48	50	50	53	47	54	53	54	58	60	56	54	50	71	68	82	65	65	68	67	68	67	65	65	72	73	73	80	82	82	79	79	75	76	79	86	73	85	83	87	89	89	85
+5	5	5	5	5	5	5	12	12	12	12	11	5	22	23	15	24	17	21	17	22	18	22	24	23	25	28	28	28	31	31	31	35	36	35	31	31	41	41	41	40	41	41	41	38	53	51	27	50	49	46	46	52	53	51	58	56	51	55	59	51	65	62	71	72	70	72	66	78	65	72	69	65	70	74	74	79	77	82	77	84	72	76	83	75	72	87	75	85	90	89
\ No newline at end of file
diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells_similarities.csv b/tools/tertiary-analysis/scmap/test-data/closest_cells_similarities.csv
new file mode 100644
index 00000000..b5ce8787
--- /dev/null
+++ b/tools/tertiary-analysis/scmap/test-data/closest_cells_similarities.csv
@@ -0,0 +1,6 @@
+,Oocyte..1.RPKM.,Oocyte..2.RPKM.,Oocyte..3.RPKM.,Zygote..1.RPKM.,Zygote..2.RPKM.,Zygote..3.RPKM.,X2.cell.embryo.1..Cell.1.RPKM.,X2.cell.embryo.1..Cell.2.RPKM.,X2.cell.embryo.2..Cell.1.RPKM.,X2.cell.embryo.2..Cell.2.RPKM.,X2.cell.embryo.3..Cell.1.RPKM.,X2.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.1..Cell.1.RPKM.,X4.cell.embryo.1..Cell.2.RPKM.,X4.cell.embryo.1..Cell.3.RPKM.,X4.cell.embryo.1..Cell.4.RPKM.,X4.cell.embryo.2..Cell.1.RPKM.,X4.cell.embryo.2..Cell.2.RPKM.,X4.cell.embryo.2..Cell.3.RPKM.,X4.cell.embryo.2..Cell.4.RPKM.,X4.cell.embryo.3..Cell.1.RPKM.,X4.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.3..Cell.3.RPKM.,X4.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.1..Cell.1.RPKM.,X8.cell.embryo.1..Cell.2.RPKM.,X8.cell.embryo.1..Cell.3.RPKM.,X8.cell.embryo.1..Cell.4.RPKM.,X8.cell.embryo.2..Cell.1.RPKM.,X8.cell.embryo.2..Cell.2.RPKM.,X8.cell.embryo.2..Cell.3.RPKM.,X8.cell.embryo.2..Cell.4.RPKM.,X8.cell.embryo.2..Cell.5.RPKM.,X8.cell.embryo.2..Cell.6.RPKM.,X8.cell.embryo.2..Cell.7.RPKM.,X8.cell.embryo.2..Cell.8.RPKM.,X8.cell.embryo.3..Cell.1.RPKM.,X8.cell.embryo.3..Cell.2.RPKM.,X8.cell.embryo.3..Cell.3.RPKM.,X8.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.3..Cell.5.RPKM.,X8.cell.embryo.3..Cell.6.RPKM.,X8.cell.embryo.3..Cell.7.RPKM.,X8.cell.embryo.3..Cell.8.RPKM.,Morulae..1..Cell.1.RPKM.,Morulae..1..Cell.2.RPKM.,Morulae..1..Cell.3.RPKM.,Morulae..1..Cell.4.RPKM.,Morulae..1..Cell.5.RPKM.,Morulae..1..Cell.6.RPKM.,Morulae..1..Cell.7.RPKM.,Morulae..1..Cell.8.RPKM.,Morulae..2..Cell.1.RPKM.,Morulae..2..Cell.2.RPKM.,Morulae..2..Cell.3.RPKM.,Morulae..2..Cell.4.RPKM.,Morulae..2..Cell.5.RPKM.,Morulae..2..Cell.6.RPKM.,Morulae..2..Cell.7.RPKM.,Morulae..2..Cell.8.RPKM.,Late.blastocyst..1..Cell.1.RPKM.,Late.blastocyst..1..Cell.2.RPKM.,Late.blastocyst..1..Cell.3.RPKM.,Late.blastocyst..1..Cell.4.RPKM.,Late.blastocyst..1..Cell.5.RPKM.,Late.blastocyst..1..Cell.6.RPKM.,Late.blastocyst..1..Cell.7.RPKM.,Late.blastocyst..1..Cell.8.RPKM.,Late.blastocyst..1..Cell.9.RPKM.,Late.blastocyst..1..Cell.10.RPKM.,Late.blastocyst..1..Cell.11.RPKM.,Late.blastocyst..1..Cell.12.RPKM.,Late.blastocyst..2..Cell.1.RPKM.,Late.blastocyst..2..Cell.2.RPKM.,Late.blastocyst..2..Cell.3.RPKM.,Late.blastocyst..2..Cell.4.RPKM.,Late.blastocyst..2..Cell.5.RPKM.,Late.blastocyst..2..Cell.6.RPKM.,Late.blastocyst..2..Cell.7.RPKM.,Late.blastocyst..2..Cell.8.RPKM.,Late.blastocyst..2..Cell.9.RPKM.,Late.blastocyst..2..Cell.10.RPKM.,Late.blastocyst..3..Cell.1.RPKM.,Late.blastocyst..3..Cell.2.RPKM.,Late.blastocyst..3..Cell.3.RPKM.,Late.blastocyst..3..Cell.4.RPKM.,Late.blastocyst..3..Cell.5.RPKM.,Late.blastocyst..3..Cell.6.RPKM.,Late.blastocyst..3..Cell.7.RPKM.,Late.blastocyst..3..Cell.8.RPKM.
+1,0.974273699811975,0.973659311436167,0.974854220234444,0.97839753346497,0.979490174962032,0.980115537598401,0.976313835558767,0.976881116973313,0.975901392182175,0.977322845448825,0.976323350516014,0.976971559860292,0.976320366157395,0.969912061538871,0.968501468487668,0.971522498841011,0.964951572472287,0.972748756493633,0.971942905027406,0.972017001342311,0.980520343865064,0.978080837270881,0.980078705456514,0.979798181564745,0.966241474136935,0.969158473501728,0.968707192268454,0.969841095031548,0.974854612410912,0.976503242175562,0.979804630823918,0.976544473170974,0.969481019998013,0.976489477308787,0.979995497607925,0.979854110006233,0.981867832635268,0.974786591856287,0.973765988696476,0.977837020195143,0.982102656773436,0.970638900011281,0.974968488962187,0.969481110283021,0.950812756659853,0.96807907709823,0.91630840568286,0.970572967922616,0.969146983045072,0.963005588968003,0.972427039750112,0.726218083982927,0.969017360461502,0.974170553961338,0.964279804847546,0.957081439198935,0.956990695530537,0.947526173473035,0.961646669180513,0.963312355197477,0.929414192606584,0.945349776265469,0.931894436659203,0.928302728076479,0.93495880629305,0.928964466633903,0.935785405180646,0.946332771937332,0.944210967521674,0.935446129048361,0.957020095156881,0.936513899155052,0.941244285216586,0.869102684962689,0.880259691379051,0.937806497095698,0.924444477590199,0.937586715214649,0.931825507780561,0.881831453276571,0.926854415776569,0.941461737032717,0.819203455562143,0.918058912946314,0.932190630105853,0.860442649254729,0.858769171932451,0.899776457031776,0.922840962875508,0.909235395907432
+2,0.974227395062693,0.973708305584207,0.974899497117833,0.978102299143981,0.979456096364997,0.979830010888303,0.976313835558767,0.976881116973313,0.975901392182175,0.977322845448825,0.976141961953352,0.976971559860292,0.977169444646141,0.968632859321209,0.969962855147019,0.971570687233282,0.962781867981641,0.973352043264989,0.973313913011762,0.97371516817206,0.978715959741429,0.978491302693835,0.977900614292412,0.978098618085579,0.965901572391676,0.96762213509642,0.967166659255134,0.96917022732004,0.97535620906972,0.981356766671598,0.981594107025288,0.973647012089677,0.966674272596261,0.971840795382014,0.977367573128536,0.981736508587417,0.981581563984833,0.978995716725436,0.97887281515733,0.977590932699052,0.980577446879086,0.970674416720001,0.978633293286482,0.9666167013426,0.961455099337142,0.974656198605929,0.886192247771376,0.96909648761121,0.972651584332793,0.960582857702193,0.975688694790544,0.726218083982927,0.967506551474963,0.968553512144433,0.96090896715229,0.954286991068606,0.962974058925164,0.965563123885223,0.960697846195483,0.96718581537045,0.930610160677049,0.943163377616397,0.929873897525988,0.931748060003204,0.931498568688411,0.927838058762556,0.931932171375485,0.94066530119158,0.924181038379451,0.930558707028389,0.942950097069521,0.937908195413747,0.934499666649093,0.863446387609202,0.879994547711384,0.936171556502554,0.924492895140808,0.954013505502333,0.936823124481827,0.92540953263808,0.92340964318551,0.95754445035796,0.834354575661276,0.879056346583803,0.924251093126694,0.845855138616278,0.850451180778096,0.93525398373097,0.922373027413517,0.938184596475574
+3,0.974227395062693,0.973708305584207,0.974899497117833,0.978061108705966,0.979367253428108,0.979834788640465,0.976293636860104,0.976907817743082,0.975961272994989,0.977298240230832,0.976152456170403,0.97707883727138,0.975867598020668,0.968054552730324,0.969422118579054,0.971565621403254,0.966614030054734,0.973215540429765,0.97453875231858,0.971662719053835,0.979333569502689,0.977015106275276,0.978478848540476,0.977492349948084,0.965901572391676,0.969158473501728,0.968707192268454,0.96917022732004,0.974738029246057,0.979362998907028,0.978984860778894,0.969975239519233,0.974325447158539,0.972498624407475,0.976727934543169,0.977626471242292,0.978165595000016,0.975344268735039,0.973662158334971,0.977452843864753,0.980130429326487,0.968346146438073,0.976253723399231,0.973309043726899,0.950991686382555,0.968096476033325,0.769932283722549,0.970520527970828,0.968478100687963,0.964493691190741,0.972285524744667,0.724424734546886,0.969559396842649,0.969364813048294,0.958239742574716,0.944755601653579,0.959029210899153,0.968964013352534,0.963723725469498,0.960711969960917,0.949879991563679,0.942457767725231,0.950427652531018,0.948091129226388,0.935725154213454,0.947068372664074,0.932792955705649,0.939589564737004,0.929847717771756,0.950599081967672,0.940231698364827,0.939390494922626,0.938175389389597,0.892258057827176,0.926372907311768,0.95245650968153,0.922841768364733,0.937416110024372,0.933878349854862,0.878774403798334,0.944167607789112,0.9386829330418,0.830037046627661,0.883713143953103,0.928636951069851,0.91354245801598,0.86465693599049,0.905142929288076,0.911070328984465,0.90368380440602
+4,0.969539415685062,0.968605789622234,0.969975869820421,0.978880784666248,0.979406018332084,0.979819636687998,0.976293636860104,0.976907817743082,0.975961272994989,0.977298240230832,0.976152456170403,0.977158123689469,0.975504907093027,0.971845463336907,0.968717611521274,0.974089634658796,0.962466765893372,0.975465656487987,0.971943800547903,0.97119242926822,0.979374101604728,0.977521766279286,0.978872836298564,0.978587440716149,0.901677778225411,0.913959709902638,0.907985127055278,0.902030768525669,0.978671530947689,0.978192307670471,0.979238784057381,0.971321474747947,0.968980303768863,0.973481969288634,0.975486961467171,0.978181972782168,0.978678187490107,0.979621906242324,0.974128403229371,0.978716502143009,0.981744937126061,0.972801044963684,0.975689620451861,0.966959316216846,0.948986566381084,0.971319263416548,0.768727443566595,0.976318084716016,0.970805631956057,0.968650129057533,0.970793775012674,0.884161023476976,0.970719442393417,0.970759373457015,0.950934738414082,0.954319812221793,0.95330754783424,0.964477748195654,0.950918486076849,0.959922979512271,0.927555396997687,0.9437771153825,0.928707351218615,0.92808219850523,0.950750592495449,0.93350274882901,0.94926566952933,0.956393920629298,0.925132041515632,0.930903887242793,0.945217709861991,0.952840812423919,0.952979443495079,0.870445895624914,0.879301494600706,0.940056288784575,0.922168581618078,0.935691371123825,0.953727252746978,0.882695442430379,0.923679390847765,0.940490114703314,0.842493259966191,0.870714868881854,0.950286607540595,0.863406327186984,0.91029255303181,0.90953170360883,0.947827057697755,0.91995220676067
+5,0.969817254140101,0.968853776261972,0.970197619293394,0.978318087034013,0.979627838281045,0.980024042561525,0.976295202149367,0.976828290786279,0.975883929338091,0.977249763573001,0.976351872523261,0.97693949907673,0.97526604170817,0.969392764396105,0.972082753917933,0.971642178273325,0.968552467156621,0.973338069870808,0.971863528606473,0.972122503355528,0.978997268316807,0.97923617236902,0.979839264747073,0.979251516686122,0.966659686718798,0.967896756105275,0.967933447549113,0.969806913585835,0.97468047745194,0.980710438282431,0.982025312731671,0.97128014024715,0.96706890205021,0.972962540152019,0.975395516724131,0.979661611525658,0.979683550210502,0.977974551163681,0.974287374630885,0.98237946179117,0.983243874593188,0.971018054408192,0.976472640461107,0.965780023061505,0.945978330164468,0.970711592341039,0.769932283722549,0.968691595297259,0.97613434952757,0.964671223129065,0.970809636630709,0.906285979702711,0.975218249730247,0.969349713160305,0.957254195804566,0.961202321805244,0.949725001547038,0.961114461409559,0.96818169457648,0.958954954371243,0.927348760597144,0.958626831905064,0.937746235449935,0.931357984297373,0.930586130999952,0.928178011434049,0.932004230352453,0.939986995525448,0.927713321807214,0.930617652160185,0.940885105808506,0.939228096678575,0.934986449800834,0.916281124363921,0.898070134322662,0.939624205949276,0.943682856153952,0.934954448019127,0.931846976521991,0.884130238961299,0.924850732080359,0.943338254819263,0.902245789824747,0.885630032810907,0.923882578758893,0.859435086584732,0.849755002912366,0.912386520745386,0.925566709087199,0.917155756034819
diff --git a/tools/tertiary-analysis/scmap/test-data/index_cell.rds b/tools/tertiary-analysis/scmap/test-data/index_cell.rds
new file mode 100644
index 00000000..82ca1a61
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/index_cell.rds differ
diff --git a/tools/tertiary-analysis/scmap/test-data/index_cluster.png b/tools/tertiary-analysis/scmap/test-data/index_cluster.png
new file mode 100644
index 00000000..02676a6c
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/index_cluster.png differ
diff --git a/tools/tertiary-analysis/scmap/test-data/index_cluster.rds b/tools/tertiary-analysis/scmap/test-data/index_cluster.rds
new file mode 100644
index 00000000..ef04d854
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/index_cluster.rds differ
diff --git a/tools/tertiary-analysis/scmap/test-data/project_cluster.csv b/tools/tertiary-analysis/scmap/test-data/project_cluster.csv
new file mode 100644
index 00000000..beac605f
--- /dev/null
+++ b/tools/tertiary-analysis/scmap/test-data/project_cluster.csv
@@ -0,0 +1,91 @@
+,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
+1,Oocyte..1.RPKM.,zygote,0.994760865096957,zygote
+2,Oocyte..2.RPKM.,zygote,0.995125744257364,zygote
+3,Oocyte..3.RPKM.,zygote,0.995591648577841,zygote
+4,Zygote..1.RPKM.,2cell,0.993401179090721,2cell
+5,Zygote..2.RPKM.,2cell,0.995369354590786,2cell
+6,Zygote..3.RPKM.,2cell,0.98710411159295,2cell
+7,X2.cell.embryo.1..Cell.1.RPKM.,2cell,0.998499099285601,2cell
+8,X2.cell.embryo.1..Cell.2.RPKM.,2cell,0.998846842740487,2cell
+9,X2.cell.embryo.2..Cell.1.RPKM.,2cell,0.998606947244777,2cell
+10,X2.cell.embryo.2..Cell.2.RPKM.,2cell,0.998676368789508,2cell
+11,X2.cell.embryo.3..Cell.1.RPKM.,2cell,0.997663075228921,2cell
+12,X2.cell.embryo.3..Cell.2.RPKM.,2cell,0.99770244480819,2cell
+13,X4.cell.embryo.1..Cell.1.RPKM.,4cell,0.990134433448036,4cell
+14,X4.cell.embryo.1..Cell.2.RPKM.,4cell,0.983906001584324,4cell
+15,X4.cell.embryo.1..Cell.3.RPKM.,4cell,0.983025466176017,4cell
+16,X4.cell.embryo.1..Cell.4.RPKM.,4cell,0.986969369421969,4cell
+17,X4.cell.embryo.2..Cell.1.RPKM.,4cell,0.978600490705419,4cell
+18,X4.cell.embryo.2..Cell.2.RPKM.,4cell,0.990517207278532,4cell
+19,X4.cell.embryo.2..Cell.3.RPKM.,4cell,0.986056209223088,4cell
+20,X4.cell.embryo.2..Cell.4.RPKM.,4cell,0.988962130990086,4cell
+21,X4.cell.embryo.3..Cell.1.RPKM.,4cell,0.995116150658076,4cell
+22,X4.cell.embryo.3..Cell.2.RPKM.,4cell,0.99274523738472,4cell
+23,X4.cell.embryo.3..Cell.3.RPKM.,4cell,0.995763679518167,4cell
+24,X4.cell.embryo.3..Cell.4.RPKM.,4cell,0.995423880082539,4cell
+25,X8.cell.embryo.1..Cell.1.RPKM.,unassigned,0.589322049052091,unassigned
+26,X8.cell.embryo.1..Cell.2.RPKM.,8cell,0.927499839382219,8cell
+27,X8.cell.embryo.1..Cell.3.RPKM.,8cell,0.921141336301299,8cell
+28,X8.cell.embryo.1..Cell.4.RPKM.,unassigned,0.59175824082949,unassigned
+29,X8.cell.embryo.2..Cell.1.RPKM.,8cell,0.974849607680171,8cell
+30,X8.cell.embryo.2..Cell.2.RPKM.,8cell,0.985093729996275,8cell
+31,X8.cell.embryo.2..Cell.3.RPKM.,8cell,0.986839564389094,8cell
+32,X8.cell.embryo.2..Cell.4.RPKM.,8cell,0.96892413940019,8cell
+33,X8.cell.embryo.2..Cell.5.RPKM.,8cell,0.96431663761681,8cell
+34,X8.cell.embryo.2..Cell.6.RPKM.,8cell,0.97148526041646,8cell
+35,X8.cell.embryo.2..Cell.7.RPKM.,8cell,0.976238026438341,8cell
+36,X8.cell.embryo.2..Cell.8.RPKM.,8cell,0.980695252466275,8cell
+37,X8.cell.embryo.3..Cell.1.RPKM.,8cell,0.97966322970515,8cell
+38,X8.cell.embryo.3..Cell.2.RPKM.,8cell,0.975362675268717,8cell
+39,X8.cell.embryo.3..Cell.3.RPKM.,8cell,0.975167821442514,8cell
+40,X8.cell.embryo.3..Cell.4.RPKM.,8cell,0.982088540632061,8cell
+41,X8.cell.embryo.3..Cell.5.RPKM.,8cell,0.983236065207029,8cell
+42,X8.cell.embryo.3..Cell.6.RPKM.,8cell,0.96962809093506,8cell
+43,X8.cell.embryo.3..Cell.7.RPKM.,8cell,0.980186666445985,8cell
+44,X8.cell.embryo.3..Cell.8.RPKM.,8cell,0.965226853665217,8cell
+45,Morulae..1..Cell.1.RPKM.,16cell,0.950320842050556,16cell
+46,Morulae..1..Cell.2.RPKM.,16cell,0.979324688404905,16cell
+47,Morulae..1..Cell.3.RPKM.,8cell,0.753074916100457,8cell
+48,Morulae..1..Cell.4.RPKM.,16cell,0.975984157933152,16cell
+49,Morulae..1..Cell.5.RPKM.,16cell,0.978965252255204,16cell
+50,Morulae..1..Cell.6.RPKM.,16cell,0.972542473750977,16cell
+51,Morulae..1..Cell.7.RPKM.,16cell,0.980084685003656,16cell
+52,Morulae..1..Cell.8.RPKM.,8cell,0.701585854974489,8cell
+53,Morulae..2..Cell.1.RPKM.,16cell,0.980419529105244,16cell
+54,Morulae..2..Cell.2.RPKM.,16cell,0.980851332000861,16cell
+55,Morulae..2..Cell.3.RPKM.,16cell,0.964267219512788,16cell
+56,Morulae..2..Cell.4.RPKM.,16cell,0.957787782168123,16cell
+57,Morulae..2..Cell.5.RPKM.,16cell,0.965485721368535,16cell
+58,Morulae..2..Cell.6.RPKM.,16cell,0.957697139912933,16cell
+59,Morulae..2..Cell.7.RPKM.,16cell,0.958777912908415,16cell
+60,Morulae..2..Cell.8.RPKM.,16cell,0.973138715636811,16cell
+61,Late.blastocyst..1..Cell.1.RPKM.,blast,0.946030792526566,blast
+62,Late.blastocyst..1..Cell.2.RPKM.,blast,0.962138004343889,blast
+63,Late.blastocyst..1..Cell.3.RPKM.,blast,0.950748704451565,blast
+64,Late.blastocyst..1..Cell.4.RPKM.,blast,0.957227580718105,blast
+65,Late.blastocyst..1..Cell.5.RPKM.,blast,0.95434894493587,blast
+66,Late.blastocyst..1..Cell.6.RPKM.,blast,0.955943421895937,blast
+67,Late.blastocyst..1..Cell.7.RPKM.,blast,0.956356985705706,blast
+68,Late.blastocyst..1..Cell.8.RPKM.,blast,0.970493175210153,blast
+69,Late.blastocyst..1..Cell.9.RPKM.,blast,0.945326349715578,blast
+70,Late.blastocyst..1..Cell.10.RPKM.,blast,0.956481724858848,blast
+71,Late.blastocyst..1..Cell.11.RPKM.,blast,0.956159281369748,blast
+72,Late.blastocyst..1..Cell.12.RPKM.,blast,0.96425809974187,blast
+73,Late.blastocyst..2..Cell.1.RPKM.,blast,0.954566650006314,blast
+74,Late.blastocyst..2..Cell.2.RPKM.,blast,0.859795704593317,blast
+75,Late.blastocyst..2..Cell.3.RPKM.,blast,0.881194674798541,blast
+76,Late.blastocyst..2..Cell.4.RPKM.,blast,0.96703530306384,blast
+77,Late.blastocyst..2..Cell.5.RPKM.,blast,0.958079246177835,blast
+78,Late.blastocyst..2..Cell.6.RPKM.,blast,0.959780240457135,blast
+79,Late.blastocyst..2..Cell.7.RPKM.,blast,0.957562095748124,blast
+80,Late.blastocyst..2..Cell.8.RPKM.,blast,0.908172032074667,blast
+81,Late.blastocyst..2..Cell.9.RPKM.,blast,0.958716824617989,blast
+82,Late.blastocyst..2..Cell.10.RPKM.,blast,0.966000611704395,blast
+83,Late.blastocyst..3..Cell.1.RPKM.,blast,0.830150497819373,blast
+84,Late.blastocyst..3..Cell.2.RPKM.,blast,0.894937328405391,blast
+85,Late.blastocyst..3..Cell.3.RPKM.,blast,0.948131108497039,blast
+86,Late.blastocyst..3..Cell.4.RPKM.,blast,0.832148158277939,blast
+87,Late.blastocyst..3..Cell.5.RPKM.,blast,0.840068518192648,blast
+88,Late.blastocyst..3..Cell.6.RPKM.,blast,0.923562228265187,blast
+89,Late.blastocyst..3..Cell.7.RPKM.,blast,0.9377231069535,blast
+90,Late.blastocyst..3..Cell.8.RPKM.,blast,0.917408664281774,blast
diff --git a/tools/tertiary-analysis/scmap/test-data/select_features.png b/tools/tertiary-analysis/scmap/test-data/select_features.png
new file mode 100644
index 00000000..a7b69da1
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/select_features.png differ
diff --git a/tools/tertiary-analysis/scmap/test-data/select_features.rds b/tools/tertiary-analysis/scmap/test-data/select_features.rds
new file mode 100644
index 00000000..8e6e608b
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/select_features.rds differ
diff --git a/tools/tertiary-analysis/scmap/test-data/test_sce.rds b/tools/tertiary-analysis/scmap/test-data/test_sce.rds
new file mode 100644
index 00000000..0d958ad0
Binary files /dev/null and b/tools/tertiary-analysis/scmap/test-data/test_sce.rds differ