Mercurial > repos > ebi-gxa > scmap_scmap_cell

comparison scmap_scmap_cell.xml @ 7:5e6d54e2ab89 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 87e6fbd3764e43b31eaa9baf9df5692eb83c8fdc"
author ebi-gxa
date Wed, 06 May 2020 06:31:53 -0400
parents 19f2fc7a8920
children 5c94e80e428f
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6:35d8f7d62659 7:5e6d54e2ab89
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 24
25 <conditional name="cluster_projection"> 25 <conditional name="cluster_projection">
26 <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."/> 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."/>
27 <when value="true" > 27 <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." /> 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." />
29 </when> 29 </when>
30 <when value="false" > 30 <when value="false" >
31 <param name="cluster_col" type="hidden" value="NULL" /> 31 <param name="cluster_col" type="hidden" value="NULL" />
35 <outputs> 35 <outputs>
36 <data name="output_single_cell_experiment" format="rdata" /> 36 <data name="output_single_cell_experiment" format="rdata" />
37 <data name="closest_cells_text_file" format="csv" /> 37 <data name="closest_cells_text_file" format="csv" />
38 <data name="closest_cells_similarities_text_file" format="csv" /> 38 <data name="closest_cells_similarities_text_file" format="csv" />
39 <data name="closest_cells_clusters_csv" format="csv"> 39 <data name="closest_cells_clusters_csv" format="csv">
40 <filter>cluster_projection == "true"</filter> 40 <filter>cluster_projection['do_cluster_projection'] == "true"</filter>
41 </data> 41 </data>
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test> 44 <test>
45 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> 45 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>