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annotate garnett_train_classifier.xml @ 0:24a22971dd44 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author ebi-gxa
date Wed, 08 Apr 2020 06:28:28 -0400
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children 2067ebe66b55
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24a22971dd44 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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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[
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8 garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --marker-file-gene-id-type '${marker_file_gene_id_type}' --num-unknown '${num_unknown}' --min-observations '${min_observations}' --max-training-samples '${max_training_samples}' --propogate-markers '${propogate_markers}' --cores '${cores}' --classifier-gene-id-type '${classifier_gene_id_type}' --output-path '${output_classifier_path}'
24a22971dd44 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
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12 <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types.
24a22971dd44 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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13 See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
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14 <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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15 <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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16 <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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17 <param type="integer" name="num_unknown" value='500' label="number of outputs" help="Number of outgroups to compare against" />
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18 <param type="integer" name="min_observations" value='8' label="Min num of observations" help="The minimum number of representative cells per
24a22971dd44 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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19 cell type required to include the cell type in the predictive model" />
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20 <param type="integer" name="max_training_samples" value='500' label="Max num of training samples" help="The maximum number of representative cells per cell
24a22971dd44 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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21 type to be included in the model training. Decreasing this number
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22 increases speed, but may hurt performance of the model." />
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23 <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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24 in finding representatives of the parent type?" />
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25 <param type="integer" name="cores" label="cores" value="1" help="The number of cores to use for computation" />
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26 <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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27 </inputs>
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28 <outputs>
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29 <data name="output_classifier_path" format="rdata" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="cds_object" value="garnett_cds.rds" />
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34 <param name="marker_file_path" value="markers_upd.txt" />
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35 <output name="output_classifier_path" value="trained_classifier.rds" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 @HELP@
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40
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41 @VERSION_HISTORY@
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42 ]]></help>
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43 <expand macro="citations" />
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44 </tool>
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45
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