Mercurial > repos > ebi-gxa > scmap_index_cluster
diff scmap_index_cluster.xml @ 3:9b60d5972dbd draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
| author | ebi-gxa |
|---|---|
| date | Fri, 24 Apr 2020 11:25:27 -0400 |
| parents | 63f1a27dce34 |
| children | b65f8ef6ca30 |
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--- a/scmap_index_cluster.xml Fri Apr 03 06:35:36 2020 -0400 +++ b/scmap_index_cluster.xml Fri Apr 24 11:25:27 2020 -0400 @@ -5,10 +5,14 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cluster.R --input-object-file "${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' + scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' + #if $train_id + --train-id '${train_id}' + #end if ]]></command> <inputs> <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'" /> + <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" /> <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." /> </inputs> <outputs>