Mercurial > repos > ebi-gxa > scpred_predict_labels

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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 13:46:06 +0000
parents eca76dd511f4
children
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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}" --normalise-data "${normalise_data}" --recompute-alignment "${recompute_alignment}" --reference-scaling "${reference_scaling}" --output-path "${output_path}"
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9
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10 #if $normalisation_method
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11 --normalisation-method "${normalisation_method}"
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12 #end if
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13 #if $scale_factor
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14 --scale-factor "${scale_factor}"
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15 #end if
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16 #if $threshold_level
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17 --threshold-level "${threshold_level}"
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18 #end if
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19 #if $max_iter_harmony
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20 --max-iter-harmony "${max_iter_harmony}"
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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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26 <param type="data" name="input_object" label="Input Seurat Object" format="rdata" help="Input Seurat object in .rds format" />
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27 <param type="data" name="pred_data" label="Query Data Matrix" format="rdata" help="Path to the input prediction matrix in .rds format"/>
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28 <param type="boolean" checked="false" name="normalise_data" label="Normalise Data" help="Should the predicted expression data be normalised? Default: False"/>
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29 <param type="text" name="normalisation_method" optional="true" value="LogNormalize" label="Normalisation Method" help="What normalisation method should be applied to predicted data? Default: LogNormalize" />
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30 <param type="integer" name="scale_factor" optional="true" value="1000000" label="Scale Factor" help="What scale factor should be applied? Note: for CPM normalisation, 1e6 is selected by default" />
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31 <param type="float" name="threshold_level" optional="true" value="0.8" label="Threshold Level" help="Classification threshold value" />
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32 <param type="integer" name="max_iter_harmony" optional="true" value="20" label="Max Iterations" help="Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step" />
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33 <param type="boolean" checked="true" name="recompute_alignment" label="Recompute Alignment" help="Recompute alignment? Useful if scPredict() has already been run. Default: True"/>
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34 <param type="boolean" checked="true" name="reference_scaling" label="Reference Scaling" help="Scale new dataset based on means and stdevs from reference dataset before alignment. Default: True"/>
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35
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36 </inputs>
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37 <outputs>
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38 <data name="output_path" format="rdata" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_object" value="scPred_trained.rds" />
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43 <param name="normalise_data" value="True" />
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44 <param name="pred_data" value="query_pbmc.rds" />
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45 <output name="output_path" file="predicted_data.rds" compare="sim_size" delta="10000000"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 @HELP@
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51 @VERSION_HISTORY@
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52 ]]></help>
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53 <expand macro="citations" />
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54 </tool>