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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author ebi-gxa
date Tue, 23 Apr 2024 07:49:19 +0000
parents dd0b44bd359a
children
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1 <tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</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-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
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9 scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' --remove-mat '${remove_mat}'
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10 #if $train_id
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11 --train-id '${train_id}'
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12 #end if
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13 #if $n_chunks
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14 --number-chunks '$n_chunks'
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15 #end if
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16 #if $n_clusters
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17 --number-clusters '$n_clusters'
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18 #end if
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19
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
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23 <param name="n_chunks" type="integer" label="Number of chunks" optional="true" value="0" help="Number of chunks into which the expr matrix is split" />
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24 <param name="n_clusters" type="integer" label="Number of clusters" optional="true" value="0" help="Number of clusters per group for k-means clustering" />
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25 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
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26 <param type="boolean" name="remove_mat" checked="false" label="Remove Matrix" help="Should the expression data be removed after classifier is trained?" />
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27 <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
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28 </inputs>
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29 <outputs>
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30 <data name="output_single_cell_experiment" format="rdata" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
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35 <param name="remove_mat" value="true" />
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36 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size" delta="10000000"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 @HELP@
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42 @VERSION_HISTORY@
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>