Mercurial > repos > ebi-gxa > scmap_scmap_cell

comparison scmap_scmap_cell.xml @ 13:48400c291093 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author ebi-gxa
date Tue, 23 Apr 2024 07:48:26 +0000
parents 65b719530dd5
children
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12:65b719530dd5 13:48400c291093
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 scmap-scmap-cell.R 8 scmap-scmap-cell.R
9 -i '$index_single_cell_experiment' 9 -i '$index_single_cell_experiment'
10 -p '$project_single_cell_experiment' 10 -p '$project_single_cell_experiment'
11 --number-nearest-neighbours '$n_nearest_neighbours' 11 --number-nearest-neighbours '$n_nearest_neighbours'
12 --nearest-neighbours-threshold '$nearest_neighbours_threshold'
13 --threshold '$threshold'
12 --cluster-col '${cluster_projection.cluster_col}' 14 --cluster-col '${cluster_projection.cluster_col}'
13 --output-object-file '$output_single_cell_experiment' 15 --output-object-file '$output_single_cell_experiment'
14 --closest-cells-text-file '$closest_cells_text_file' 16 --closest-cells-text-file '$closest_cells_text_file'
15 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file' 17 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
16 #if $cluster_projection 18 #if $cluster_projection
19 ]]></command> 21 ]]></command>
20 <inputs> 22 <inputs>
21 <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." /> 23 <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." />
22 <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'" /> 24 <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'" />
23 <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" /> 25 <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" />
26 <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." />
27 <param name="threshold" type="integer" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
24 <conditional name="cluster_projection"> 28 <conditional name="cluster_projection">
25 <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."/> 29 <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."/>
26 <when value="true" > 30 <when value="true" >
27 <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." /> 31 <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." />
28 </when> 32 </when>
41 </outputs> 45 </outputs>
42 <tests> 46 <tests>
43 <test> 47 <test>
44 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> 48 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
45 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/> 49 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
46 <param name="cluster_projection" value="true" /> 50 <conditional name="cluster_projection">
51 <param name="do_cluster_projection" value="true" />
52 <param name="cluster_col" value="cell_type1" />
53 </conditional>
47 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/> 54 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
48 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" /> 55 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
49 <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/> 56 <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
50 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/> 57 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
58 </test>
59 <test>
60 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
61 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
62 <conditional name="cluster_projection">
63 <param name="do_cluster_projection" value="true" />
64 <param name="cluster_col" value="cell_type1" />
65 </conditional>
66 <param name="nearest_neighbours_threshold" value="3" />
67 <param name="threshold" value="0.5" />
68 <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/>
69 <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" />
70 <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/>
71 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/>
51 </test> 72 </test>
52 </tests> 73 </tests>
53 <help><![CDATA[ 74 <help><![CDATA[
54 @HELP@ 75 @HELP@
55 76