Mercurial > repos > ebi-gxa > scmap_scmap_cell

comparison scmap_scmap_cell.xml @ 0:cb6b70d45519 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author ebi-gxa
date Mon, 16 Sep 2019 09:56:58 -0400
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children 2b85cec412c3
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-1:000000000000 0:cb6b70d45519
1 <tool id="scmap_scmap_cell" name="scmap cell projection" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
2 <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>
3 <macros>
4 <import>scmap_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 scmap-scmap-cell.R
9 -i '$index_single_cell_experiment'
10 -p '$project_single_cell_experiment'
11 --number-nearest-neighbours '$n_nearest_neighbours'
12 --cluster-col '${cluster_projection.cluster_col}'
13 --output-object-file '$output_single_cell_experiment'
14 --closest-cells-text-file '$closest_cells_text_file'
15 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
16 #if $cluster_projection
17 --output-clusters-text-file '$closest_cells_clusters_csv'
18 #end if
19 ]]></command>
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." />
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" />
24
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."/>
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." />
29 </when>
30 <when value="false" >
31 <param name="cluster_col" type="hidden" value="NULL" />
32 </when>
33 </conditional>
34 </inputs>
35 <outputs>
36 <data name="output_single_cell_experiment" format="rdata" />
37 <data name="closest_cells_text_file" format="csv" />
38 <data name="closest_cells_similarities_text_file" format="csv" />
39 <data name="closest_cells_clusters_csv" format="csv">
40 <filter>cluster_projection == "true"</filter>
41 </data>
42 </outputs>
43 <tests>
44 <test>
45 <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"/>
47 <param name="cluster_projection" value="true" ftype="rdata"/>
48 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds"/>
49 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" />
50 <output name="closest_cells_text_file" file="closest_cells.csv"/>
51 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv"/>
52 </test>
53 </tests>
54 <help><![CDATA[
55 @HELP@
56
57 @VERSION_HISTORY@
58 ]]></help>
59 <expand macro="citations" />
60 </tool>