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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
author ebi-gxa
date Mon, 27 Apr 2020 11:19:44 -0400
parents 2067ebe66b55
children 9be21507358d
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1 <tool id="garnett_train_classifier" name="Garnett - train classifier" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Train classifier based on marker gene list</description>
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3 <macros>
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4 <import>garnett_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[
1
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8 garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cores \${GALAXY_SLOTS:-1} --output-path '${output_classifier_path}'
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9 #if $train_id
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10 --train-id '${train_id}'
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11 #end if
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12 #if $cds_gene_id_type
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13 --cds-gene-id-type '${cds_gene_id_type}'
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14 #end if
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15 #if $marker_file_gene_id_type
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16 --marker-file-gene-id-type '${marker_file_gene_id_type}'
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17 #end if
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18 #if $num_unknown
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19 --num-unknown '${num_unknown}'
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20 #end if
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21 #if $min_observations
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22 --min-observations '${min_observations}'
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23 #end if
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24 #if $max_training_samples
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25 --max-training-samples '${max_training_samples}'
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26 #end if
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27 #if $propogate_markers
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28 --propogate-markers '${propogate_markers}'
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29 #end if
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30 #if $classifier_gene_id_type
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31 --classifier-gene-id-type '${classifier_gene_id_type}'
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
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36 <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types.
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37 See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
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38 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
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39 <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
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40 <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
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41 <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" />
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42 <param type="integer" name="num_unknown" value='500' label="number of outputs" help="Number of outgroups to compare against" />
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43 <param type="integer" name="min_observations" value='8' label="Min num of observations" help="The minimum number of representative cells per
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44 cell type required to include the cell type in the predictive model" />
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45 <param type="integer" name="max_training_samples" value='500' label="Max num of training samples" help="The maximum number of representative cells per cell
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46 type to be included in the model training. Decreasing this number
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47 increases speed, but may hurt performance of the model." />
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48 <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used
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49 in finding representatives of the parent type?" />
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50 <param type="text" name="classifier_gene_id_type" label="Classifier gene ID type" value="ENSEMBL" help="The type of gene ID that will be used in the classifier. If possible for your organism, this should be 'ENSEMBL', which is the default." />
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51 </inputs>
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52 <outputs>
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53 <data name="output_classifier_path" format="rdata" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="cds_object" value="garnett_cds.rds" />
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58 <param name="marker_file_path" value="markers_upd.txt" />
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59 <output name="output_classifier_path" value="trained_classifier.rds" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 @HELP@
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64
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65 @VERSION_HISTORY@
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66 ]]></help>
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67 <expand macro="citations" />
1
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68 </tool>