Mercurial > repos > ebi-gxa > garnett_transform_markers
diff garnett_transform_markers.xml @ 0:2142ecf6ff02 draft
"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 06:18:13 -0400 |
| parents | |
| children | 211241c50ccf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/garnett_transform_markers.xml Wed Apr 08 06:18:13 2020 -0400 @@ -0,0 +1,35 @@ +<tool id="garnett_transform_markers" name="Garnett - transform markes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett</description> + <macros> + <import>garnett_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}' --pval-col '${pval_col}' --pval-threshold '${pval_threshold}' --groups-col '${groups_col}' --gene-names '${gene_names}' --garnett-marker-file '${garnett_marker_file}' + ]]></command> + <inputs> + <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" /> + <param type="data" name="marker_list" format="rdata" label="Marker list object" help="Path to a serialised object containing marker genes" /> + <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" /> + <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" /> + <param type="text" name="groups_col" value="groups" label="groups column" help="Column name of cell groups (i.e. cluster IDs or cell types) in marker file" /> + <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" /> + </inputs> + <outputs> + <data name="garnett_marker_file" format="txt" /> + </outputs> + <tests> + <test> + <param name="input_marker_file" value="ref_marker_genes.txt" /> + <param name="marker_list" value="marker_list.rds" /> + <output name="garnett_marker_file" file="markers_transformed.txt" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> +