annotate scpred_train_test_split.xml @ 5:bb71ba86e806 draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit e2e8344bd707659bcb2bdfcfdda648179884bd53"
author ebi-gxa
date Fri, 14 Aug 2020 11:09:40 -0400
parents 9c7ec345c4c9
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1 <tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>CPM normalise and partition into train/test data</description>
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3 <macros>
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4 <import>scpred_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 scpred_train_test_split.R --input-sce-object "${input_sce_object}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --training-labels "${training_labs}" --cell-types-column "${cell_types_col}" --test-labels "${test_labs}"
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10 #if $norm_counts_slot
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11 --normalised-counts-slot "${norm_counts_slot}"
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12 #end if
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13 #if $training_ratio
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14 --training-ratio "${training_ratio}"
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15 #end if
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17 ]]></command>
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18 <inputs>
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19 <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
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20 <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
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21 <param type="text" name="cell_types_col" label="Column name for assigned cell types" />
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22 <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" />
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23 </inputs>
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24 <outputs>
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25 <data name="training_mat" format="rdata" />
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26 <data name="test_mat" format="rdata" />
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27 <data name="training_labs" format="txt" />
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28 <data name="test_labs" format="txt" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_sce_object" value="pollen_cpm.rds" />
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33 <param name="cell_types_col" value="cell_type2" />
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34 <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/>
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35 <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/>
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36 <output name="training_labs" file="train_metadata.txt" compare="sim_size" />
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37 <output name="test_labs" file="test_metadata.txt" compare="sim_size" />
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 @HELP@
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42
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43 @VERSION_HISTORY@
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44 ]]></help>
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45 <expand macro="citations" />
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46 </tool>