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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 07:48:14 +0000
parents a0da1d3155dd
children
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1 <tool id="scmap_scmap_cluster" name="Scmap cluster projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>projects one dataset to another</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-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
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12 <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
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13 <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
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14 </inputs>
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15 <outputs>
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16 <data name="output_single_cell_experiment" format="rdata" label="${tool.name} on ${on_string}: RDS object"/>
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17 <data name="output_txt" format="tabular" label="${tool.name} on ${on_string}: table"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
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22 <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
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23 <output name="output_single_cell_experiment">
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24 <assert_contents>
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25 <has_size value="6100k" delta="500k"/>
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26 </assert_contents>
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27 </output>
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28 <output name="output_txt">
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29 <assert_contents>
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30 <has_n_lines n="91"/>
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31 <has_text text="zygote"/>
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32 </assert_contents>
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33 </output>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 @HELP@
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38
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39 @VERSION_HISTORY@
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40 ]]></help>
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41 <expand macro="citations" />
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42 </tool>