ebi-gene-expression-group · pcm32 · Apr 23, 2024 · Nov 19, 2023 · Nov 21, 2023 · Nov 21, 2023
diff --git a/tools/tertiary-analysis/scmap/scmap_get_std_output.xml b/tools/tertiary-analysis/scmap/scmap_get_std_output.xml
@@ -5,7 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}"  --tool '${tool}' --sim-col-name "${sim_col_name}"
+        scmap_get_std_output.R
+        --predictions-file "${input_predictions_file}"
+        --output-table "${output_predictions_file}"
+        --include-scores "${include_scores}"
+        --tool '${tool}'
+        --sim-col-name "${sim_col_name}"
         #if $index
           --index "${index}"
         #end if   
@@ -21,13 +26,19 @@
         <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
     </inputs>
     <outputs>
-        <data name="output_predictions_file" format="txt" />
+        <data name="output_predictions_file" format="tabular" />
     </outputs>
     <tests>
         <test>
             <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
             <param name="include_scores" value="TRUE" />
-            <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
+            <output name="output_predictions_file">
+                <assert_contents>
+                    <has_n_lines n="92"/>
+                    <has_text text="predicted_label"/>
+                    <has_text text="Zygote..3.RPKM."/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git 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
@@ -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/scmap_scmap_cluster.xml b/tools/tertiary-analysis/scmap/scmap_scmap_cluster.xml
@@ -13,15 +13,24 @@
         <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
     </inputs>
     <outputs>
-        <data name="output_single_cell_experiment" format="rdata" />
-        <data name="output_txt" format="tabular" />
+        <data name="output_single_cell_experiment" format="rdata" label="${tool.name} on ${on_string}: RDS object"/>
+        <data name="output_txt" format="tabular" label="${tool.name} on ${on_string}: table"/>
     </outputs>
     <tests>
         <test>
             <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
             <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
-            <output name="output_single_cell_experiment" file="project_cluster.rds" compare="sim_size"/>
-            <output name="output_txt" file="project_cluster.tsv" compare="sim_size"/>
+            <output name="output_single_cell_experiment">
+                <assert_contents>
+                    <has_size value="6100k" delta="500k"/>
+                </assert_contents>
+            </output>
+            <output name="output_txt">
+                <assert_contents>
+                    <has_n_lines n="91"/>
+                    <has_text text="zygote"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/tertiary-analysis/scmap/scmap_select_features.xml b/tools/tertiary-analysis/scmap/scmap_select_features.xml
@@ -5,7 +5,14 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-select-features.R --input-object-file "${input_single_cell_experiment}.preprocessed" --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        scmap-preprocess-sce.R 
+         --input-object "${input_single_cell_experiment}"
+         --output-sce-object "result.preprocessed" && 
+        scmap-select-features.R 
+         --input-object-file "result.preprocessed"
+         --n-features '$n_features'
+         --output-object-file '$output_single_cell_experiment'
+         --output-plot-file '$plot'
     ]]></command>
     <inputs>
         <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />

diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells.csv 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
diff --git a/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv b/tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv
@@ -0,0 +1,91 @@
+cell	scmap_cluster_labs	scmap_cluster_siml	combined_labs
+Oocyte..1.RPKM.	zygote	0.972457633278923	zygote
+Oocyte..2.RPKM.	zygote	0.972353568313767	zygote
+Oocyte..3.RPKM.	zygote	0.973371064673993	zygote
+Zygote..1.RPKM.	zygote	0.97866272698663	zygote
+Zygote..2.RPKM.	zygote	0.979717800854604	zygote
+Zygote..3.RPKM.	zygote	0.97984002400711	zygote
+X2.cell.embryo.1..Cell.1.RPKM.	2cell	0.975860542596827	2cell
+X2.cell.embryo.1..Cell.2.RPKM.	2cell	0.975977483944058	2cell
+X2.cell.embryo.2..Cell.1.RPKM.	2cell	0.97534563242085	2cell
+X2.cell.embryo.2..Cell.2.RPKM.	2cell	0.976532855604968	2cell
+X2.cell.embryo.3..Cell.1.RPKM.	2cell	0.975715675528499	2cell
+X2.cell.embryo.3..Cell.2.RPKM.	2cell	0.976512040050606	2cell
+X4.cell.embryo.1..Cell.1.RPKM.	4cell	0.976740874886324	4cell
+X4.cell.embryo.1..Cell.2.RPKM.	4cell	0.970679786566831	4cell
+X4.cell.embryo.1..Cell.3.RPKM.	4cell	0.971937340916803	4cell
+X4.cell.embryo.1..Cell.4.RPKM.	4cell	0.974396302382197	4cell
+X4.cell.embryo.2..Cell.1.RPKM.	4cell	0.968256593061058	4cell
+X4.cell.embryo.2..Cell.2.RPKM.	4cell	0.976000962530563	4cell
+X4.cell.embryo.2..Cell.3.RPKM.	4cell	0.974456795916042	4cell
+X4.cell.embryo.2..Cell.4.RPKM.	4cell	0.975046287156331	4cell
+X4.cell.embryo.3..Cell.1.RPKM.	4cell	0.980907467386254	4cell
+X4.cell.embryo.3..Cell.2.RPKM.	4cell	0.979702774175472	4cell
+X4.cell.embryo.3..Cell.3.RPKM.	4cell	0.979541752074044	4cell
+X4.cell.embryo.3..Cell.4.RPKM.	4cell	0.979397781619405	4cell
+X8.cell.embryo.1..Cell.1.RPKM.	8cell	0.965866705260469	8cell
+X8.cell.embryo.1..Cell.2.RPKM.	8cell	0.971874515954174	8cell
+X8.cell.embryo.1..Cell.3.RPKM.	8cell	0.970182782492083	8cell
+X8.cell.embryo.1..Cell.4.RPKM.	8cell	0.971803309754166	8cell
+X8.cell.embryo.2..Cell.1.RPKM.	8cell	0.975660495961879	8cell
+X8.cell.embryo.2..Cell.2.RPKM.	8cell	0.978697234565528	8cell
+X8.cell.embryo.2..Cell.3.RPKM.	8cell	0.980500043303112	8cell
+X8.cell.embryo.2..Cell.4.RPKM.	8cell	0.973337322820485	8cell
+X8.cell.embryo.2..Cell.5.RPKM.	8cell	0.97050828475866	8cell
+X8.cell.embryo.2..Cell.6.RPKM.	8cell	0.97427362884691	8cell
+X8.cell.embryo.2..Cell.7.RPKM.	8cell	0.977362207861906	8cell
+X8.cell.embryo.2..Cell.8.RPKM.	8cell	0.978677072589576	8cell
+X8.cell.embryo.3..Cell.1.RPKM.	8cell	0.97989418833849	8cell
+X8.cell.embryo.3..Cell.2.RPKM.	8cell	0.97485334405104	8cell
+X8.cell.embryo.3..Cell.3.RPKM.	8cell	0.975859793936309	8cell
+X8.cell.embryo.3..Cell.4.RPKM.	8cell	0.981490977097	8cell
+X8.cell.embryo.3..Cell.5.RPKM.	8cell	0.981029618769028	8cell
+X8.cell.embryo.3..Cell.6.RPKM.	8cell	0.969682040359692	8cell
+X8.cell.embryo.3..Cell.7.RPKM.	8cell	0.978148246228053	8cell
+X8.cell.embryo.3..Cell.8.RPKM.	8cell	0.970328380893092	8cell
+Morulae..1..Cell.1.RPKM.	16cell	0.959918851368306	16cell
+Morulae..1..Cell.2.RPKM.	16cell	0.973499865778146	16cell
+Morulae..1..Cell.3.RPKM.	16cell	0.905095452914499	16cell
+Morulae..1..Cell.4.RPKM.	16cell	0.975565450656408	16cell
+Morulae..1..Cell.5.RPKM.	16cell	0.972676900609201	16cell
+Morulae..1..Cell.6.RPKM.	16cell	0.965520701954854	16cell
+Morulae..1..Cell.7.RPKM.	16cell	0.974360238512134	16cell
+Morulae..1..Cell.8.RPKM.	16cell	0.89292960975856	16cell
+Morulae..2..Cell.1.RPKM.	16cell	0.973068555642167	16cell
+Morulae..2..Cell.2.RPKM.	16cell	0.972782844321894	16cell
+Morulae..2..Cell.3.RPKM.	16cell	0.964788103357924	16cell
+Morulae..2..Cell.4.RPKM.	16cell	0.966128218632723	16cell
+Morulae..2..Cell.5.RPKM.	16cell	0.959906305241092	16cell
+Morulae..2..Cell.6.RPKM.	16cell	0.973292643125946	16cell
+Morulae..2..Cell.7.RPKM.	16cell	0.972824053645381	16cell
+Morulae..2..Cell.8.RPKM.	16cell	0.966191355651732	16cell
+Late.blastocyst..1..Cell.1.RPKM.	blast	0.954545456827362	blast
+Late.blastocyst..1..Cell.2.RPKM.	blast	0.959479973403999	blast
+Late.blastocyst..1..Cell.3.RPKM.	blast	0.95220936077016	blast
+Late.blastocyst..1..Cell.4.RPKM.	blast	0.950460474784597	blast
+Late.blastocyst..1..Cell.5.RPKM.	blast	0.952198095399196	blast
+Late.blastocyst..1..Cell.6.RPKM.	blast	0.947932383616434	blast
+Late.blastocyst..1..Cell.7.RPKM.	blast	0.953028259974652	blast
+Late.blastocyst..1..Cell.8.RPKM.	blast	0.955242273190534	blast
+Late.blastocyst..1..Cell.9.RPKM.	blast	0.945069684662869	blast
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