Mercurial > repos > ebi-gxa > scmap_index_cluster
comparison scmap_index_cluster.xml @ 1:e6d99b0652ec draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
author | ebi-gxa |
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date | Fri, 25 Oct 2019 08:45:05 -0400 |
parents | 6b24ebf5b7fb |
children | 63f1a27dce34 |
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0:6b24ebf5b7fb | 1:e6d99b0652ec |
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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-cluster.R --input-object-file '$input_single_cell_experiment' --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' | 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cluster.R --input-object-file "preprocessed_${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' |
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="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." /> | 12 <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." /> |
13 </inputs> | 13 </inputs> |