Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_umap.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:11:27 +0000 |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 <tool id="signac_umap" name="Calculate UMAP" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> embedding of scATAC-seq data.</description> | |
| 3 <macros> | |
| 4 <import>signac_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" /> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 11 Rscript '${__tool_directory__}'/signac-umap.R --signac-object $signac_object --reduction $reduction_use --dims-use $dims_use --output-object-file $rds_signac_seurat_file | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 15 <param type="text" name="reduction_use" value='lsi' label="Dimensional reduction to use for UMAP (default:lsi)." help='Which dimensional reduction (PCA or ICA) to use for the UMAP input.'/> | |
| 16 <param type="text" name="dims_use" value='2,30' label="Dimensional reduction to use for UMAP (default:lsi)." help='How many dimensions to use for UMAP.'/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (UMAP)"/> | |
| 20 </outputs> | |
| 21 <help><![CDATA[ | |
| 22 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object. | |
| 23 ]]></help> | |
| 24 </tool> |