annotate scpred_eigen_decomp.xml @ 2:70e5a19d9d7e draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f1471c41f9845cce8b58a51089dcf096c39fe8d6"
author ebi-gxa
date Mon, 01 Jun 2020 09:20:45 -0400
parents 3867289e6c1a
children 9ccb6e5d6781
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1 <tool id="scpred_eigen_decompose" name="Scpred eigen-decompose" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Perform matrix eigen-decomposition; initialize object of scPred class</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_eigen_decomp.R --training-matrix "${training_matrix}" --training-labels "${training_labels}" --output-path "${output_object_path}"
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9
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10 #if $log_transform
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11 --log-transform "${log_transform}"
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12 #end if
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13 #if $principal_components
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14 --principal-comps "${principal_components}"
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15 #end if
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16 ]]></command>
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17 <inputs>
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18 <param type="data" name="training_matrix" label="Training matrix" format="rdata" help="Training matrix obtained from train/test split step" />
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19 <param type="boolean" name="log_transform" label="log-transform" checked="True" help="Should log-transform be performed on training data?" />
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20 <param type="data" name="training_labels" label="training labels file" format="txt" help="Path to training labels in text format" />
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21 <param type="integer" name="principal_components" label="Number of pincipal components" value="10" help="Number of principal components" />
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22 </inputs>
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23 <outputs>
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24 <data name="output_object_path" format="rdata" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="training_matrix" value="train_matrix.mtx" />
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29 <param name="training_labels" value="train_metadata.txt" />
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30 <output name="output_object_path" file="scPred_object.rds" compare="sim_size" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 @HELP@
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35
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36 @VERSION_HISTORY@
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37 ]]></help>
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38 <expand macro="citations" />
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39 </tool>