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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:45:33 +0000
parents 41a316354ffb
children
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41a316354ffb "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_get_feature_space' name='ScPred feature space' version='@TOOL_VERSION@+galaxy0' profile="@PROFILE@">
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2 <description>Get feature space for training matrix</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_get_feature_space.R --input-object '${input_object}' --prediction-column '${prediction_column}' --output-path '${output_obj_path}'
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10 #if $correction_method
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11 --correction-method '${correction_method}'
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12 #end if
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13 #if $significance_threshold
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14 --significance-threshold '${significance_threshold}'
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15 #end if
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16 #if $reduction_parameter
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17 --reduction-parameter '${reduction_parameter}'
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18 #end if
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21 ]]></command>
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22 <inputs>
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23 <param type='data' name='input_object' label='Input Seurat object' format='rdata' help='Input Seurat object in .rds format' />
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24 <param type='text' name='prediction_column' optional="true" value="cell_type" label='Prediction Column' help='Name of the metadata column that contains training labels' />
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25 <param type='text' name='correction_method' label='Correction Method' optional='true' value="fdr" help='Method for mulpiple testing correction' />
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26 <param type='float' name='significance_threshold' label='Significance Threshold' optional='true' value="1.0" help='Significance threshold for principal components explaining class identity' />
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27 <param type='text' name='reduction_parameter' label='Reduction Parameter' optional='true' value="pca" help='Name of reduction in Seurat objet to be used to determine the feature space. Default: "pca"' />
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28
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29 </inputs>
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30 <outputs>
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31 <data name='output_obj_path' format='rdata' />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_object" value="reference_pbmc.rds" />
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36 <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
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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>