Mercurial > repos > ebi-gxa > scmap_scmap_cell

comparison scmap_scmap_cell.xml @ 12:65b719530dd5 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:44:11 +0000
parents 1543a50e08c9
children 48400c291093
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11:1543a50e08c9 12:65b719530dd5
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <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." /> 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." />
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'" /> 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'" />
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" /> 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" />
24
25 <conditional name="cluster_projection"> 24 <conditional name="cluster_projection">
26 <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."/> 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."/>
27 <when value="true" > 26 <when value="true" >
28 <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." /> 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." />
29 </when> 28 </when>
41 </data> 40 </data>
42 </outputs> 41 </outputs>
43 <tests> 42 <tests>
44 <test> 43 <test>
45 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> 44 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
46 <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/> 45 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
47 <param name="cluster_projection" value="true" ftype="rdata"/> 46 <param name="cluster_projection" value="true" />
48 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/> 47 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
49 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" compare="sim_size" /> 48 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
50 <output name="closest_cells_text_file" file="closest_cells.csv" compare="sim_size"/> 49 <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
51 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv" compare="sim_size"/> 50 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
52 </test> 51 </test>
53 </tests> 52 </tests>
54 <help><![CDATA[ 53 <help><![CDATA[
55 @HELP@ 54 @HELP@
56 55