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Add parameters to Scmap #310

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Add parameters to Scmap #310

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865b160
Update scmap_scmap_cell.xml
hexhowells Nov 19, 2023
fe42d3f
Add new test
hexhowells Nov 21, 2023
4f12b70
Update tool version
hexhowells Nov 21, 2023
00fd8f4
Try with fully qualified name of variable.
pcm32 Feb 13, 2024
081d77a
Add fully qualified name variable to second test
hexhowells Feb 13, 2024
cf19525
Correctly implement conditional parameters in tests
hexhowells Feb 13, 2024
29b8dd1
Re-add test data
hexhowells Feb 26, 2024
b161f79
convert closest_cell_clusters to TSV
hexhowells Feb 26, 2024
6bf2400
add missing images
hexhowells Feb 26, 2024
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5 changes: 3 additions & 2 deletions tools/tertiary-analysis/scmap/scmap_macros.xml
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@@ -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>
Expand All @@ -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.
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23 changes: 22 additions & 1 deletion tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
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Expand Up @@ -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'
Expand All @@ -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" >
Expand All @@ -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@
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6 changes: 6 additions & 0 deletions tools/tertiary-analysis/scmap/test-data/closest_cells.csv
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,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
Binary file added tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.rds
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6 changes: 6 additions & 0 deletions tools/tertiary-analysis/scmap/test-data/closest_cells_clusters.tsv
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Original file line number Diff line number Diff line change
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 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
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