| Next changeset 1:2067ebe66b55 (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_macros.xml garnett_train_classifier.xml |
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| diff -r 000000000000 -r 24a22971dd44 garnett_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_macros.xml Wed Apr 08 06:28:28 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" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ + **Version history** + 0.2.8+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{, + url = {https://doi.org/10.1038/s41592-019-0535-3}, + author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell}, + title = {Supervised classification enables rapid annotation of cell atlases}, + journal = {Nature Methods} + } + </citation> + <citation type="bibtex"> + @misc{githubgarnett-cli.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2019}, + title = {garnett-cli: command line interface for Garnett tool}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/garnett-cli.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> + |
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| diff -r 000000000000 -r 24a22971dd44 garnett_train_classifier.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_train_classifier.xml Wed Apr 08 06:28:28 2020 -0400 |
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| @@ -0,0 +1,46 @@ +<tool id="garnett_train_classifier" name="Garnett - train classifier" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Train classifier based on marker gene list</description> + <macros> + <import>garnett_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + garnett_train_classifier.R --cds-object '${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}' + ]]></command> + <inputs> + <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" /> + <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types. + See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" /> + <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="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" /> + <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" /> + <param type="integer" name="num_unknown" value='500' label="number of outputs" help="Number of outgroups to compare against" /> + <param type="integer" name="min_observations" value='8' label="Min num of observations" help="The minimum number of representative cells per + cell type required to include the cell type in the predictive model" /> + <param type="integer" name="max_training_samples" value='500' label="Max num of training samples" help="The maximum number of representative cells per cell + type to be included in the model training. Decreasing this number + increases speed, but may hurt performance of the model." /> + <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used + in finding representatives of the parent type?" /> + <param type="integer" name="cores" label="cores" value="1" help="The number of cores to use for computation" /> + <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." /> + </inputs> + <outputs> + <data name="output_classifier_path" format="rdata" /> + </outputs> + <tests> + <test> + <param name="cds_object" value="garnett_cds.rds" /> + <param name="marker_file_path" value="markers_upd.txt" /> + <output name="output_classifier_path" value="trained_classifier.rds" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> + + |