Mercurial > repos > ebi-gxa > scmap_scmap_cell

annotate 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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1 <tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>
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3 <macros>
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4 <import>scmap_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 scmap-scmap-cell.R
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9 -i '$index_single_cell_experiment'
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10 -p '$project_single_cell_experiment'
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11 --number-nearest-neighbours '$n_nearest_neighbours'
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12 --nearest-neighbours-threshold '$nearest_neighbours_threshold'
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13 --threshold '$threshold'
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14 --cluster-col '${cluster_projection.cluster_col}'
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15 --output-object-file '$output_single_cell_experiment'
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16 --closest-cells-text-file '$closest_cells_text_file'
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17 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
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18 #if $cluster_projection
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19 --output-clusters-text-file '$clusters_text_file'
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20 #end if
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21 ]]></command>
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22 <inputs>
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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." />
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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'" />
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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" />
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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." />
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27 <param name="threshold" type="float" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
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28 <conditional name="cluster_projection">
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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."/>
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30 <when value="true" >
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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." />
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32 </when>
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33 <when value="false" >
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34 <param name="cluster_col" type="hidden" value="NULL" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="output_single_cell_experiment" format="rdata" />
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40 <data name="closest_cells_text_file" format="tabular" />
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41 <data name="closest_cells_similarities_text_file" format="tabular" />
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42 <data name="clusters_text_file" format="tabular">
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43 <filter>cluster_projection['do_cluster_projection']</filter>
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
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49 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
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50 <conditional name="cluster_projection">
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51 <param name="do_cluster_projection" value="true" />
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52 <param name="cluster_col" value="cell_type1" />
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53 </conditional>
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54 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
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55 <output name="clusters_text_file">
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56 <assert_contents>
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57 <has_n_lines n="91" delta="1"/>
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58 <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
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59 <has_text_matching expression="Zygote..3.RPKM.\tunassigned\tNA\tunassigned"/>
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60 <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
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61 <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
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62 <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
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63 <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
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64 <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
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65 </assert_contents>
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66 </output>
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67 <output name="closest_cells_text_file" file="closest_cells.tsv"/>
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68 <output name="closest_cells_similarities_text_file">
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69 <assert_contents>
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70 <has_n_lines n="6"/>
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71 <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
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72 <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
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73 <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
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74 <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
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75 <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
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76 </assert_contents>
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77 </output>
0
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78 </test>
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79 <test>
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80 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
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81 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
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82 <conditional name="cluster_projection">
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83 <param name="do_cluster_projection" value="true" />
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84 <param name="cluster_col" value="cell_type1" />
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85 </conditional>
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86 <param name="nearest_neighbours_threshold" value="1" />
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87 <param name="threshold" value="0.2" />
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88 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
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89 <output name="clusters_text_file">
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90 <assert_contents>
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91 <has_n_lines n="91" delta="1"/>
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92 <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
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93 <has_text_matching expression="Zygote..3.RPKM.\tzygote\t0\.980.*\tzygote"/>
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94 <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
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95 <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
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96 <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
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97 <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
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98 <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
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99 </assert_contents>
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100 </output>
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101 <output name="closest_cells_text_file" file="closest_cells.tsv"/>
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102 <output name="closest_cells_similarities_text_file">
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103 <assert_contents>
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104 <has_n_lines n="6"/>
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105 <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
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106 <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
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107 <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
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108 <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
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109 <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
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110 </assert_contents>
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111 </output>
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112 </test>
0
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113 </tests>
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114 <help><![CDATA[
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115 @HELP@
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116
0
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117 @VERSION_HISTORY@
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>