Mercurial > repos > ebi-gxa > scpred_predict_labels

annotate scpred_predict.xml @ 5:eca76dd511f4 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bb88d0eb9c193518eb0d05321e3458a10212d3ab"
author ebi-gxa
date Fri, 14 Aug 2020 10:47:23 -0400
parents fd06ab29487f
children b869bb6d4b01
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eca76dd511f4 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bb88d0eb9c193518eb0d05321e3458a10212d3ab"
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1 <tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy0">
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2 <description>Make cell type predictions using trained model.</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_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --output-path "${output_tbl_path}"
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10 #if $test_labels
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11 --test-labels "${test_labels}"
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12 #end if
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13 #if $cell_types_column
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14 --cell-types-column "${cell_types_column}"
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15 #end if
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16 #if $plot_path
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17 --plot-path "${plot_path}"
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18 #end if
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19 #if $confusion_table
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20 --confusion-table "${confusion_table}"
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21 #end if
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22
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23 ]]></command>
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24 <inputs>
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25 <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
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26 <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
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27 <param type="data" name="test_labels" optional="true" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />
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28 <param type="text" name="cell_types_column" value="cell_type2" optional="true" label="Cell types column name" help="Column name of true labels in provided metadata file" />
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29 </inputs>
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30 <outputs>
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31 <data name="output_tbl_path" format="txt" />
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32 <data name="plot_path" format="png" />
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33 <data name="confusion_table" format="txt" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input_object" value="scPred_trained.rds" />
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38 <param name="pred_data" value="test_matrix.mtx" />
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39 <param name="test_labels" value="test_metadata.txt" />
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40 <output name="output_tbl_path" file="predictions_table.txt" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 @HELP@
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45
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46 @VERSION_HISTORY@
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>