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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 07:48:41 +0000
parents 4ff68faee6e1
children
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1 <tool id="scmap_index_cluster" name="Scmap index clusters" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>calculates centroids of each cell type and merges them into a single table</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 "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
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9 --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 ]]></command>
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14 <inputs>
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15 <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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16 <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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17 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
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18 <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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19 </inputs>
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20 <outputs>
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21 <data name="output_single_cell_experiment" format="rdata" />
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22 <data name="plot" format="png" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
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27 <param name="remove_mat" value="true" />
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28 <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size" delta="1000000000"/>
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29 <output name="plot" file="index_cluster.png" compare="sim_size" delta="1000000000"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 @HELP@
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34
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35 @VERSION_HISTORY@
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36 ]]></help>
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37 <expand macro="citations" />
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38 </tool>