Mercurial > repos > ebi-gxa > garnett_transform_markers
comparison garnett_transform_markers.xml @ 2:b35eef6b1fcc draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
| author | ebi-gxa |
|---|---|
| date | Mon, 27 Apr 2020 09:34:03 -0400 |
| parents | 211241c50ccf |
| children | 1dc49d16e96c |
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| 1:211241c50ccf | 2:b35eef6b1fcc |
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| 20 --gene-names '${gene_names}' | 20 --gene-names '${gene_names}' |
| 21 #end if | 21 #end if |
| 22 ]]></command> | 22 ]]></command> |
| 23 <inputs> | 23 <inputs> |
| 24 <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" /> | 24 <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" /> |
| 25 <param type="data" name="marker_list" format="rdata" label="Marker list object" help="Path to a serialised object containing marker genes" /> | |
| 26 <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" /> | 25 <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" /> |
| 27 <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" /> | 26 <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" /> |
| 28 <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" /> | 27 <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" /> |
| 29 <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" /> | 28 <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" /> |
| 30 </inputs> | 29 </inputs> |
| 31 <outputs> | 30 <outputs> |
| 32 <data name="garnett_marker_file" format="txt" /> | 31 <data name="garnett_marker_file" format="txt" /> |
| 32 <data name="marker_list" format="rdata" /> | |
| 33 </outputs> | 33 </outputs> |
| 34 <tests> | 34 <tests> |
| 35 <test> | 35 <test> |
| 36 <param name="input_marker_file" value="ref_marker_genes.txt" /> | 36 <param name="input_marker_file" value="ref_marker_genes.txt" /> |
| 37 <param name="marker_list" value="marker_list.rds" /> | 37 <param name="marker_list" value="marker_list.rds" /> |