| Next changeset 1:a16b409dee64 (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49" |
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added:
garnett_get_feature_genes.xml garnett_macros.xml |
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| diff -r 000000000000 -r 29117f5b2cd9 garnett_get_feature_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_get_feature_genes.xml Wed Apr 08 06:29:13 2020 -0400 |
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| @@ -0,0 +1,25 @@ +<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 '${classifier_object}' --node '${node}' --database '${database}' --convert-ids '${convert_ids}' --output-path '${output_path}' + ]]></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> \ No newline at end of file |
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| diff -r 000000000000 -r 29117f5b2cd9 garnett_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_macros.xml Wed Apr 08 06:29:13 2020 -0400 |
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| @@ -0,0 +1,44 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.8</token> + <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token> + <token name="@PROFILE@">18.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.3">garnett-cli</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + echo $(R --version | grep version | grep -v GNU)", garnett version" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ + **Version history** + 0.2.8+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{, + url = {https://doi.org/10.1038/s41592-019-0535-3}, + author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell}, + title = {Supervised classification enables rapid annotation of cell atlases}, + journal = {Nature Methods} + } + </citation> + <citation type="bibtex"> + @misc{githubgarnett-cli.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2019}, + title = {garnett-cli: command line interface for Garnett tool}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/garnett-cli.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> + |