Mercurial > repos > ebi-gxa > scmap_index_cell
comparison scmap_index_cell.xml @ 1:17b3d7e04b3c draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
| author | ebi-gxa |
|---|---|
| date | Fri, 25 Oct 2019 08:44:38 -0400 |
| parents | 628a433819c6 |
| children | dd2a84734b87 |
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| 0:628a433819c6 | 1:17b3d7e04b3c |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <import>scmap_macros.xml</import> | 4 <import>scmap_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 8 scmap-index-cell.R --input-object-file '$input_single_cell_experiment' --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' | 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cell.R --input-object-file "preprocessed_${input_single_cell_experiment}" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' |
| 9 ]]></command> | 9 ]]></command> |
| 10 <inputs> | 10 <inputs> |
| 11 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" /> | 11 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" /> |
| 12 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" /> | 12 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" /> |
| 13 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" /> | 13 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" /> |