Mercurial > repos > ebi-gxa > garnett_get_feature_genes
view garnett_get_feature_genes.xml @ 2:3176cbad2800 draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
author | ebi-gxa |
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date | Mon, 27 Apr 2020 11:20:02 -0400 |
parents | a16b409dee64 |
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<tool id="garnett_get_feature_genes" name="Garnett - get feature genes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Obtain a list of genes used as features in classification model</description> <macros> <import>garnett_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ garnett_get_feature_genes.R --classifier-object '${classifier_object}' --database '${database}' --output-path '${output_path}' #if $node --node '${node}' #end if #if $convert_ids --convert-ids '${convert_ids}' #end if ]]></command> <inputs> <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" /> <param type="text" name="node" label="node" value="root" help="In case a hierarchical marker tree was used to train the classifier, specify which node features should be shown. Default is 'root'. For other nodes, use the corresponding parent cell type name" /> <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" /> <param type="boolean" name="convert_ids" checked="false" label="convert gene IDs" help="Boolean that indicates whether the gene IDs should be converted into SYMBOL notation" /> </inputs> <outputs> <data name="output_path" format="txt" /> </outputs> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>