Mercurial > repos > ebi-gxa > garnett_check_markers
diff garnett_check_markers.xml @ 0:d2aace2bb87f draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author | ebi-gxa |
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date | Wed, 08 Apr 2020 06:17:49 -0400 |
parents | |
children | c00e672eadbc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_check_markers.xml Wed Apr 08 06:17:49 2020 -0400 @@ -0,0 +1,39 @@ +<tool id="garnett_check_markers" name="Garnett - check markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Check marker file to filter out markers of suboptimal quality</description> + <macros> + <import>garnett_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + garnett_check_markers.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 '${marker_file_gene_id_type}' --marker-output-path '${marker_output_path}' --plot-output-path '${plot_output_path}' --propogate-markers '${propogate_markers}' --classifier-gene-id-type '${classifier_gene_id_type}' + ]]></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="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="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="marker_output_path" format="txt" /> + <data name="plot_output_path" format="png" /> + </outputs> + <tests> + <test> + <param name="cds_object" value="garnett_cds.rds" /> + <param name="marker_file_path" value="markers_transformed.txt" /> + <output name="marker_output_path" value="marker_check.txt" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> +