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comparison scmap_scmap_cell.xml @ 14:32ae4a600167 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9dbf2be568a0cea589fee8a42f070718d7966780-dirty
author ebi-gxa
date Mon, 08 Jul 2024 08:53:18 +0000
parents 48400c291093
children
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13:48400c291093 14:32ae4a600167
1 <tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description> 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> 3 <macros>
4 <import>scmap_macros.xml</import> 4 <import>scmap_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
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 '$nearest_neighbours_threshold' 12 --nearest-neighbours-threshold '$nearest_neighbours_threshold'
13 --threshold '$threshold' 13 --threshold '$threshold'
14 --cluster-col '${cluster_projection.cluster_col}' 14 --cluster-col '${cluster_projection.cluster_col}'
15 --output-object-file '$output_single_cell_experiment' 15 --output-object-file '$output_single_cell_experiment'
16 --closest-cells-text-file '$closest_cells_text_file' 16 --closest-cells-text-file '$closest_cells_text_file'
17 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file' 17 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
18 #if $cluster_projection 18 #if $cluster_projection
19 --output-clusters-text-file '$closest_cells_clusters_csv' 19 --output-clusters-text-file '$clusters_text_file'
20 #end if 20 #end if
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
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." /> 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." />
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'" /> 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'" />
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" /> 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." /> 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)." /> 27 <param name="threshold" type="float" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
28 <conditional name="cluster_projection"> 28 <conditional name="cluster_projection">
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."/> 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."/>
30 <when value="true" > 30 <when value="true" >
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." /> 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." />
32 </when> 32 </when>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="output_single_cell_experiment" format="rdata" /> 39 <data name="output_single_cell_experiment" format="rdata" />
40 <data name="closest_cells_text_file" format="tabular" /> 40 <data name="closest_cells_text_file" format="tabular" />
41 <data name="closest_cells_similarities_text_file" format="tabular" /> 41 <data name="closest_cells_similarities_text_file" format="tabular" />
42 <data name="closest_cells_clusters_csv" format="tabular"> 42 <data name="clusters_text_file" format="tabular">
43 <filter>cluster_projection['do_cluster_projection']</filter> 43 <filter>cluster_projection['do_cluster_projection']</filter>
44 </data> 44 </data>
45 </outputs> 45 </outputs>
46 <tests> 46 <tests>
47 <test> 47 <test>
50 <conditional name="cluster_projection"> 50 <conditional name="cluster_projection">
51 <param name="do_cluster_projection" value="true" /> 51 <param name="do_cluster_projection" value="true" />
52 <param name="cluster_col" value="cell_type1" /> 52 <param name="cluster_col" value="cell_type1" />
53 </conditional> 53 </conditional>
54 <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"/>
55 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" /> 55 <output name="clusters_text_file">
56 <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/> 56 <assert_contents>
57 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/> 57 <has_n_lines n="91" delta="1"/>
58 <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
59 <has_text_matching expression="Zygote..3.RPKM.\tunassigned\tNA\tunassigned"/>
60 <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
61 <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
62 <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
63 <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
64 <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
65 </assert_contents>
66 </output>
67 <output name="closest_cells_text_file" file="closest_cells.tsv"/>
68 <output name="closest_cells_similarities_text_file">
69 <assert_contents>
70 <has_n_lines n="6"/>
71 <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
72 <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
73 <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
74 <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
75 <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
76 </assert_contents>
77 </output>
58 </test> 78 </test>
59 <test> 79 <test>
60 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> 80 <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"/> 81 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
62 <conditional name="cluster_projection"> 82 <conditional name="cluster_projection">
63 <param name="do_cluster_projection" value="true" /> 83 <param name="do_cluster_projection" value="true" />
64 <param name="cluster_col" value="cell_type1" /> 84 <param name="cluster_col" value="cell_type1" />
65 </conditional> 85 </conditional>
66 <param name="nearest_neighbours_threshold" value="3" /> 86 <param name="nearest_neighbours_threshold" value="1" />
67 <param name="threshold" value="0.5" /> 87 <param name="threshold" value="0.2" />
68 <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/> 88 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
69 <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" /> 89 <output name="clusters_text_file">
70 <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/> 90 <assert_contents>
71 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/> 91 <has_n_lines n="91" delta="1"/>
92 <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
93 <has_text_matching expression="Zygote..3.RPKM.\tzygote\t0\.980.*\tzygote"/>
94 <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
95 <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
96 <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
97 <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
98 <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
99 </assert_contents>
100 </output>
101 <output name="closest_cells_text_file" file="closest_cells.tsv"/>
102 <output name="closest_cells_similarities_text_file">
103 <assert_contents>
104 <has_n_lines n="6"/>
105 <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
106 <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
107 <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
108 <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
109 <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
110 </assert_contents>
111 </output>
72 </test> 112 </test>
73 </tests> 113 </tests>
74 <help><![CDATA[ 114 <help><![CDATA[
75 @HELP@ 115 @HELP@
76 116
77 @VERSION_HISTORY@ 117 @VERSION_HISTORY@
78 ]]></help> 118 ]]></help>
79 <expand macro="citations" /> 119 <expand macro="citations" />
80 </tool> 120 </tool>