Mercurial > repos > ebi-gxa > scmap_scmap_cell
view scmap_scmap_cell.xml @ 6:35d8f7d62659 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f1d792b2db8e09e441cc75629d34a13e4fb19153"
author | ebi-gxa |
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date | Mon, 04 May 2020 07:14:30 -0400 |
parents | 19f2fc7a8920 |
children | 5e6d54e2ab89 |
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<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description> <macros> <import>scmap_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ scmap-scmap-cell.R -i '$index_single_cell_experiment' -p '$project_single_cell_experiment' --number-nearest-neighbours '$n_nearest_neighbours' --cluster-col '${cluster_projection.cluster_col}' --output-object-file '$output_single_cell_experiment' --closest-cells-text-file '$closest_cells_text_file' --closest-cells-similarities-text-file '$closest_cells_similarities_text_file' #if $cluster_projection --output-clusters-text-file '$closest_cells_clusters_csv' #end if ]]></command> <inputs> <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" /> <conditional name="cluster_projection"> <param name="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" > <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." /> </when> <when value="false" > <param name="cluster_col" type="hidden" value="NULL" /> </when> </conditional> </inputs> <outputs> <data name="output_single_cell_experiment" format="rdata" /> <data name="closest_cells_text_file" format="csv" /> <data name="closest_cells_similarities_text_file" format="csv" /> <data name="closest_cells_clusters_csv" format="csv"> <filter>cluster_projection == "true"</filter> </data> </outputs> <tests> <test> <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/> <param name="cluster_projection" value="true" ftype="rdata"/> <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/> <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" compare="sim_size" /> <output name="closest_cells_text_file" file="closest_cells.csv" compare="sim_size"/> <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv" compare="sim_size"/> </test> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>